Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process

ABSTRACT

The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.

This application is a continuation of U.S. patent application Ser. No.15/216,783, filed Jul. 22, 2016, which is a divisional of U.S. patentapplication Ser. No. 13/487,637, filed Jun. 4, 2012, which is acontinuation of U.S. patent application Ser. No. 12/716,681, filed Mar.3, 2010, now U.S. Pat. No. 8,206,913, which is a continuation-in-part(CIP) application that claims priority to U.S. patent application Ser.No. 10/795,667, filed Mar. 8, 2004, now U.S. Pat. No. 7,718,403, whichclaims priority to U.S. Provisional Patent Application Ser. No.60/453,060, filed Mar. 7, 2003, and this CIP application also claimspriority to U.S. Provisional Patent Application Ser. No. 61/157,165,filed Mar. 3, 2009, all of which applications are incorporated byreference herein in their entirety.

The sequence listing that is contained in the file named“RUBCP0022USCP1C1D1 ST25.txt”, which is 41 KB (as measured in MicrosoftWindows®) and was created on Jul. 12, 2016, is incorporated by referenceherein.

FIELD OF THE INVENTION

The present invention is directed to the fields of genomics, molecularbiology, genotyping, and expression profiling. In some embodiments, thepresent invention relates to methods for the amplification of DNA orcDNA yielding a product that is a non-biased representation of theoriginal genomic or transcribed sequences, wherein the methods utilizeprimers substantially incapable of forming primer dimers.

BACKGROUND OF THE INVENTION

For genomic studies, the quality and quantity of DNA samples is crucial.High-throughput genetic analysis requires large amounts of template fortesting. However, the amount of DNA extracted from individual patientsamples, for example, is limited. DNA sample size also limits forensicand paleobiology work. Thus, there has been a concerted effort indeveloping methods to amplify the entire genome. The goal of wholegenome amplification (WGA) is to supply a sufficient amount of genomicsequence for a variety of procedures, as well as long-term storage forfuture work and archiving of patient samples. There is a clear need toamplify entire genomes in an automatable, robust, representativefashion. Whole genome amplification has historically been accomplishedusing one of three techniques: polymerase chain reaction (PCR), stranddisplacement, or cell immortalization.

PCR™

PCR™ is a powerful technique to amplify DNA (Saiki, 1985). This in vitrotechnique amplifies DNA by repeated thermal denaturation, primerannealing and polymerase extension, thereby amplifying a single targetDNA molecule to detectable quantities. PCR™ is not amenable to theamplification of long DNA molecules such as entire chromosomes, which inhumans are approximately 10⁸ bases in length. The commonly usedpolymerase in PCR reactions is Taq polymerase, which cannot amplifyregions of DNA larger than about 5000 bases. Moreover, knowledge of theexact nucleotide sequences flanking the amplification target isnecessary in order to design primers used in the PCR reaction.

Whole Genome PCR™

Whole genome PCR™ results in the amplification either of complete poolsof DNA or of unknown intervening sequences between specific primerbinding sites. The amplification of complete pools of DNA, termed knownamplification (Lüdecke et al., 1989) or general amplification (Teleniuset al., 1992), can be achieved by different means. Common to allapproaches is the capability of the PCR™ system to unanimously amplifyDNA fragments in the reaction mixture without preference for specificDNA sequences. The structure of primers used for whole genome PCR™ isdescribed as totally degenerate (i.e., all nucleotides are termed N,N=A, T, G, C), partially degenerate (i.e., several nucleotides aretermed N) or non-degenerate (i.e., all positions exhibit definednucleotides).

Whole genome PCR™ involves converting total genomic DNA to a form whichcan be amplified by PCR (Kinzler and Vogelstein, 1989). In thistechnique, total genomic DNA is fragmented via shearing or enzymaticdigestion with, for instance, a restriction enzyme such as MboI, to anaverage size of 200-300 base pairs. The ends of the DNA are made bluntby incubation with the Klenow fragment of DNA polymerase. The DNAfragments are ligated to catch linkers consisting of a 20 base pair DNAfragment synthesized in vitro. The catch linkers consist of twophosphorylated oligomers: 5′-GAGTAGAATTCTAATATCTA-3′ (SEQ ID NO:1) and5′-GAGATATTAGAATTCTACTC-3′ (SEQ ID NO:2). To select against the “catch”linkers that were self-ligated, the ligation product is cleaved withXhoI. Each catch linker has one half of an XhoI site at its termini;therefore, XhoI cleaves catch linkers ligated to themselves but will notcleave catch linkers ligated to most genomic DNA fragments. The linkedDNA is in a form that can be amplified by PCR™ using the catch oligomersas primers. The DNA of interest can then be selected via binding to aspecific protein or nucleic acid and recovered. The small amount of DNAfragments specifically bound can be amplified using PCR™. The steps ofselection and amplification may be repeated as often as necessary toachieve the desired purity. Although 0.5 ng of starting DNA wasamplified 5000-fold, Kinzler and Vogelstein (1989) did report a biastoward the amplification of smaller fragments.

Whole Genome PCR™ with Non-Degenerate Primers

Lone Linker PCR™

Because of the inefficiency of the conventional catch linkers due toself-hybridization of two complementary primers, asymmetrical linkersfor the primers were designed (Ko et al., 1990). The sequences of thecatch linker oligonucleotides (Kinzler and Vogelstein, 1989) were usedwith the exception of a deleted 3 base pair sequence from the 3′-end ofone strand. This “lone-linker” has both a non-palindromic protruding endand a blunt end, thus preventing multimerization of linkers. Moreover,as the orientation of the linker was defined, a single primer wassufficient for amplification. After digestion with a four-base cuttingenzyme, the lone linkers were ligated. Lone-linker PCR™ (LL-PCR™)produces fragments ranging from 100 bases to −2 kb that were reported tobe amplified with similar efficiency.

Interspersed Repetitive Sequence PCR

As used for the general amplification of DNA, interspersed repetitivesequence PCR™ (IRS-PCR™) uses non-degenerate primers that are based onrepetitive sequences within the genome. This allows for amplification ofsegments between suitable positioned repeats and has been used to createhuman chromosome- and region-specific libraries (Nelson et al., 1989).IRS-PCR™ is also termed Alu element mediated-PCR™ (ALU-PCR™), which usesprimers based on the most conserved regions of the Alu repeat family andallows the amplification of fragments flanked by these sequences (Nelsonet al., 1989). A major disadvantage of IRS-PCR™ is that abundantrepetitive sequences like the Alu family are not uniformly distributedthroughout the human genome, but preferentially found in certain areas(e.g., the light bands of human chromosomes) (Korenberg and Rykowski,1988). Thus, IRS-PCR™ results in a bias toward these regions and a lackof amplification of other, less represented areas. Moreover, thistechnique is dependent on the knowledge of the presence of abundantrepeat families in the genome of interest.

Linker Adapter PCR™

The limitations of IRS-PCR™ are abated to some extent using the linkeradapter technique (LA-PCR™) (Lüdecke et al., 1989; Saunders et al.,1989; Kao and Yu, 1991). This technique amplifies unknown restricted DNAfragments with the assistance of ligated duplex oligonucleotides (linkeradapters). DNA is commonly digested with a frequently cuttingrestriction enzyme such as RsaI, yielding fragments that are on average500 bp in length. After ligation, PCR™ can be performed using primerscomplementary to the sequence of the adapters. Temperature conditionsare selected to enhance annealing specifically to the complementary DNAsequences, which leads to the amplification of unknown sequencessituated between the adapters. Post-amplification, the fragments arecloned. There should be little sequence selection bias with LA-PCR™except on the basis of distance between restriction sites. Methods ofLA-PCR™ overcome the hurdles of regional bias and species dependencecommon to IRS-PCR™. However, LA-PCR is technically more challenging thanother whole genome amplification (WGA) methods.

A large number of band-specific microdissection libraries of human,mouse, and plant chromosomes have been established using LA-PCR™ (Changet al., 1992; Wesley et al., 1990; Saunders et al., 1989; Vooijs et al.,1993; Hadano et al., 1991; Miyashita et al., 1994). PCR™ amplificationof a microdissected region of a chromosome is conducted by digestionwith a restriction enzyme (e.g., Sau3A, MboI) to generate a number ofshort fragments, which are ligated to linker-adapter oligonucleotidesthat provide priming sites for PCR™ amplification (Saunders et al.,1989). Two oligonucleotides, a 20-mer and a 24-mer creating a 5′overhang that was phosphorylated with T4 polynucleotide kinase andcomplementary to the end generated by the restriction enzyme, were mixedin equimolar amounts and allowed to anneal. Following thisamplification, as much as 1 μg of DNA can be amplified from as little asone band dissected from a polytene chromosome (Saunders et al., 1989;Johnson, 1990). Ligation of a linker-adapter to each end of thechromosomal restriction fragment provides the primer-binding sitenecessary for in vitro semiconservative DNA replication. Otherapplications of this technology include amplification of one flow-sortedmouse chromosome 11 and use of resulting DNA library as a probe inchromosome painting (Miyashita et al., 1994), and amplification of DNAof a single flow-sorted chromosome (VanDeanter et al., 1994).

A different adapter used in PCR™ is the Vectorette (Riley et al., 1990).This technique is largely used for the isolation of terminal sequencesfrom yeast artificial chromosomes (YAC) (Kleyn et al., 1993; Naylor etal., 1993; Valdes et al., 1994). Vectorette is a syntheticoligonucleotide duplex containing an overhang complementary to theoverhang generated by a restriction enzyme. The duplex contains a regionof non-complementarity as a primer-binding site. After ligation ofdigested YACs and a Vectorette unit, amplification is performed betweenprimers identical to Vectorette and primers derived from the yeastvector. Products will only be generated if, in the first PCR™ cycle,synthesis has taken place from the yeast vector primer, thussynthesizing products from the termini of YAC inserts.

Priming Authorizing Random Mismatches PCR™

Another whole genome PCR™ method using non-degenerate primers is PrimingAuthorizing Random Mismatches-PCR™ (PARM-PCR™), which uses specificprimers and unspecific annealing conditions resulting in a randomhybridization of primers leading to universal amplification (Milan etal., 1993). Annealing temperatures are reduced to 30° C. for the firsttwo cycles and raised to 60° C. in subsequent cycles to specificallyamplify the generated DNA fragments. This method has been used touniversally amplify flow sorted porcine chromosomes for identificationvia fluorescent in situ hybridization (FISH) (Milan et al., 1993). Asimilar technique was also used to generate chromosome DNA clones frommicrodissected DNA (Hadano et al., 1991). In this method, a 22-merprimer unique in sequence, which randomly primes and amplifies anytarget DNA, was utilized. The primer contained recognition sites forthree restriction enzymes. Thermocycling was done in three stages: stageone had an annealing temperature of 22° C. for 120 minutes, and stagestwo and three were conducted under stringent annealing conditions.

Single Cell Comparative Genomic Hybridization

A method allowing the comprehensive analysis of the entire genome on asingle cell level has been developed termed single cell comparativegenomic hybridization (SCOMP) (Klein et al., 1999; WO 00/17390). GenomicDNA from a single cell is fragmented with a four base cutter, such asMseI, giving an expected average length of 256 bp (4⁴) based on thepremise that the four bases are evenly distributed. Ligation mediatedPCR™ was utilized to amplify the digested restriction fragments.Briefly, two primers ((5′-AGTGGGATTCCGCATGCTAGT-3′; SEQ ID NO:3); and(5′-TAACTAGCATGC-3′; SEQ ID NO:4)); were annealed to each other tocreate an adapter with two 5′ overhangs. The 5′ overhang resulting fromthe shorter oligo is complementary to the ends of the DNA fragmentsproduced by MseI cleavage. The adapter was ligated to the digestedfragments using T4 DNA ligase. Only the longer primer was ligated to theDNA fragments as the shorter primer did not have the 5′ phosphatenecessary for ligation. Following ligation, the second primer wasremoved via denaturation, and the first primer remained ligated to thedigested DNA fragments. The resulting 5′ overhangs were filled in by theaddition of DNA polymerase. The resulting mixture was then amplified byPCR™ using the longer primer.

As this method is reliant on restriction digests to fragment the genomicDNA, it is dependent on the distribution of restriction sites in theDNA. Very small and very long restriction fragments will not beeffectively amplified, resulting in a biased amplification. The averagefragment length of 256 generated by MseI cleavage will result in a largenumber of fragments that are too short to amplify.

Whole Genome PCR™ with Degenerate Primers

In order to overcome difficulties associated with many techniques usingnon-degenerate primers for universal amplification, techniques usingpartially or totally degenerate primers were developed for universalamplification of minute amounts of DNA.

Degenerate Oligonucleotide Primed PCR™

Degenerate oligonucleotide-primed PCR™ (DOP-PCR™) was developed usingpartially degenerate primers, thus providing a more generalamplification technique than IRS-PCR (Wesley et al., 1990; Telenius,1992). A system was described using non-specific primers(5′-TTGCGGCCGCATTNNNNTTC-3′ (SEQ ID NO:5); showing complete degenerationat positions 4, 5, 6, and 7 from the 3′ end (Wesley et al., 1990). Thethree specific bases at the 3′end are statistically expected tohybridize every 64 (4³) bases, thus the last seven bases will match dueto the partial degeneration of the primer. The first cycles ofamplification are conducted at a low annealing temperature (30° C.),allowing sufficient priming to initiate DNA synthesis at frequentintervals along the template. The defined sequence at the 3′ end of theprimer tends to separate initiation sites, thus increasing product size.As the PCR product molecules all contain a common specific 5′ sequence,the annealing temperature is raised to 56° C. after the first eightcycles. The system was developed to unspecifically amplifymicrodissected chromosomal DNA from Drosophila, replacing themicrocloning system of Lüdecke et al. (1989) described above.

The term DOP-PCR™ was introduced by Telenius et al. (1992) who developedthe method for genome mapping research using flow sorted chromosomes. Asingle primer is used in DOP-PCR™ as used by Wesley et al. (1990). Theprimer (5′-CCGACTCGACNNNNNATGTGG-3′ (SEQ ID NO:6); shows six specificbases on the 3′-end, a degenerate part with 6 bases in the middle and aspecific region with a rare restriction site at the 5′-end.Amplification occurs in two stages. Stage one encompasses the lowtemperature cycles. In the first cycle, the 3′-end of the primershybridize to multiple sites of the target DNA initiated by the lowannealing temperature. In the second cycle, a complementary sequence isgenerated according to the sequence of the primer. In stage two, primerannealing is performed at a temperature restricting all non-specifichybridization. Up to 10 low temperature cycles are performed to generatesufficient primer binding sites. Up to 40 high temperature cycles areadded to specifically amplify the prevailing target fragments.

DOP-PCR™ is based on the principle of priming from short sequencesspecified by the 3′-end of partially degenerate oligonucleotides usedduring initial low annealing temperature cycles of the PCR™ protocol. Asthese short sequences occur frequently, amplification of target DNAproceeds at multiple loci simultaneously. DOP-PCR™ is applicable to thegeneration of libraries containing high levels of single copy sequences,provided uncontaminated DNA in a substantial amount is obtainable (e.g.,flow-sorted chromosomes). This method has been applied to less than onenanogram of starting genomic DNA (Cheung and Nelson, 1996).

Advantages of DOP-PCR™ in comparison to systems of totally degenerateprimers are the higher efficiency of amplification, reduced chances forunspecific primer-primer binding and the availability of a restrictionsite at the 5′ end for further molecular manipulations. However,DOP-PCR™ does not claim to replicate the target DNA in its entirety(Cheung and Nelson, 1996). Moreover, as relatively short products aregenerated, specific amplification of fragments up to approximately 500bp in length are produced (Telenius et al., 1992; Cheung and Nelson,1996; Wells et al., 1999; Sanchez-Cespedes et al., 1998; Cheung et al.,1998).

In light of these limitations, a method has been described that produceslong DOP-PCR™ products ranging from 0.5 to 7 kb in size, allowing theamplification of long sequence targets in subsequent PCR (long DOP-PCR™)(Buchanan et al., 2000). However, long DOP-PCR utilizes 200 ng ofgenomic DNA, which is more DNA than most applications will haveavailable. Subsequently, a method was described that generates longamplification products from picogram quantities of genomic DNA, termedlong products from low DNA quantities DOP-PCR™ (LL-DOP-PCR™) (Kittler etal., 2002). This method achieves this by the 3′-5′ exonucleaseproofreading activity of DNA polymerase Pwo and an increased annealingand extension time during DOP-PCR™, which are necessary steps togenerate longer products. Although an improvement in success rate wasdemonstrated in comparison with other DOP-PCR™ methods, this method didhave a 15.3% failure rate due to complete locus dropout for the majorityof the failures and sporadic locus dropout and allele dropout for theremaining genotype failures. There was a significant deviation fromrandom expectations for the occurrence of failures across loci, thusindicating a locus-dependent effect on whole genome coverage.

Sequence Independent PCR™

Another approach using degenerate primers is described by Bohlander etal., (1992), called sequence-independent DNA amplification (SIA). Incontrast to DOP-PCR™, SIA incorporates a nested DOP-primer system. Thefirst primer (5′-TGGTAGCTCTTGATCANNNNN-3′ (SEQ ID NO:7); consisted of afive base random 3′-segment and a specific 16 base segment at the 5′ endcontaining a restriction enzyme site. Stage one of PCR™ starts with 97°C. for denaturation, followed by cooling down to 4° C., causing primersto anneal to multiple random sites, and then heating to 37° C. A T7 DNApolymerase is used. In the second low-temperature cycle, primers annealto products of the first round. In the second stage of PCR™, a primer(5′-AGAGTTGGTAGCTCTTGATC-3′ (SEQ ID NO:8); is used that contains, at the3′ end, 15 5′-end bases of primer A. Five cycles are performed with thisprimer at an intermediate annealing temperature of 42° C. An additional33 cycles are performed at a specific annealing temperature of 56° C.Products of SIA range from 200 bp to 800 bp.

Primer-Extension Preamplification

Primer-extension preamplification (PEP) is a method that uses totallydegenerate primers to achieve universal amplification of the genome(Zhang et al., 1992). PEP uses a random mixture of 15-base fullydegenerated oligonucleotides as primers, thus any one of the fourpossible bases could be present at each position. Theoretically, theprimer is composed of a mixture of 4×10⁹ different oligonucleotidesequences. This leads to amplification of DNA sequences from randomlydistributed sites. In each of the 50 cycles, the template is firstdenatured at 92° C. Subsequently, primers are allowed to anneal at a lowtemperature (37° C.), which is then continuously increased to 55° C. andheld for another four minutes for polymerase extension.

A method of improved PEP (I-PEP) was developed to enhance the efficiencyof PEP, primarily for the investigation of tumors from tissue sectionsused in routine pathology to reliably perform multiple microsatelliteand sequencing studies with a single or few cells (Dietmaier et al.,1999). I-PEP differs from PEP (Zhang et at, 1992) in cell lysisapproaches, improved thermal cycle conditions, and the addition of ahigher fidelity polymerase. Specifically, cell lysis is performed in ELbuffer, Taq polymerase is mixed with proofreading Pwo polymerase, and anadditional elongation step at 68° C. for 30 seconds before thedenaturation step at 94° C. was added. This method was more efficientthan PEP and DOP-PCR™ in amplification of DNA from one cell and fivecells.

Both DOP-PCR™ and PEP have been used successfully as precursors to avariety of genetic tests and assays. These techniques are integral tothe fields of forensics and genetic disease diagnosis where DNAquantities are limited. However, neither technique claims to replicateDNA in its entirety (Cheung and Nelson, 1996) or provide completecoverage of particular loci (Paunio et al., 1996). These techniquesproduce an amplified source for genotyping or marker identification. Theproducts produced by these methods are consistently short (<3 kb) and assuch cannot be used in many applications (Telenius et al., 1992).Moreover, numerous tests are required to investigate a few markers orloci.

Tagged PCR™

Tagged PCR™ (T-PCR™) was developed to increase the amplificationefficiency of PEP in order to amplify efficiently from small quantitiesof DNA samples with sizes ranging from 400 bp to 1.6 kb (Grothues etal., 1993). T-PCR™ is a two-step strategy, which uses, for the first fewlow-stringent cycles, a primer with a constant 17 base pair at the 5′end and a tagged random primer containing 9 to 15 random bases at the 3′end. In the first PCR™ step, the tagged random primer is used togenerate products with tagged primer sequences at both ends, which isachieved by using a low annealing temperature. The unincorporatedprimers are then removed and amplification is carried out with a secondprimer containing only the constant 5′ sequence of the first primerunder high-stringency conditions to allow exponential amplification.This method is more labor intensive than other methods due to therequirement for removal of unincorporated degenerate primers, which alsocan cause the loss of sample material. This is critical when workingwith subnanogram quantities of DNA template. The unavoidable loss oftemplate during the purification steps could affect the coverage ofT-PCR™. Moreover, tagged primers with 12 or more random bases couldgenerate non-specific products resulting from primer-primer extensionsor less efficient elimination of these longer primers during thefiltration step.

Tagged Random Hexamer Amplification

Based on problems related to T-PCR™, tagged random hexamer amplification(TRHA) was developed on the premise that it would be advantageous to usea tagged random primer with shorter random bases (Wong et al., 1996). InTRHA, the first step is to produce a size distributed population of DNAmolecules from a pNL1 plasmid. This was done via a random synthesisreaction using Klenow fragment and random hexamer tagged with T7 primerat the 5′-end (T7-dN₆, 5′-GTAATACGACTCACTATAGGGCNNNNNN-3 (SEQ ID NO:9).Klenow-synthesized molecules (size range 28 bp-<23 kb) were thenamplified with T7 primer (5′-GTAATACGACTCACTATAGGGC-3′ (SEQ ID NO:10).Examination of bias indicated that only 76% of the original DNA templatewas preferentially amplified and represented in the TRHA products.

Strand Displacement

The isothermal technique of rolling circle amplification (RCA) has beendeveloped for amplifying large circular DNA templates such as plasmidand bacteriophage DNA (Dean et al., 2001). Using ϕ29 DNA polymerase,which synthesizes DNA strands 70 kb in length using randomexonuclease-resistant hexamer primers, DNA was amplified in a 30° C.isothermal reaction. Secondary priming events occur on the displacedproduct DNA strands, resulting in amplification via strand displacement.

In this technique, two sets of primers are used. The right set ofprimers each have a portion complementary to nucleotide sequencesflanking one side of a target nucleotide sequence, and primers in theleft set of primers each have a portion complementary to nucleotidesequences flanking the other side of the target nucleotide sequence. Theprimers in the right set are complementary to one strand of the nucleicacid molecule containing the target nucleotide sequence, and the primersin the left set are complementary to the opposite strand. The 5′ end ofprimers in both sets is distal to the nucleic acid sequence of interestwhen the primers are hybridized to the flanking sequences in the nucleicacid molecule. Ideally, each member of each set has a portioncomplementary to a separate and non-overlapping nucleotide sequenceflanking the target nucleotide sequence. Amplification proceeds byreplication initiated at each primer and continuing through the targetnucleic acid sequence. A key feature of this method is the displacementof intervening primers during replication. Once the nucleic acid strandselongated from the right set of primers reaches the region of thenucleic acid molecule to which the left set of primers hybridizes, andvice versa, another round of priming and replication commences. Thisallows multiples copies of a nested set of the target nucleic acidsequence to be synthesized.

Multiple Displacement Amplification

The principles of RCA have been extended to WGA in a technique calledmultiple displacement amplification (MDA) (Dean et al., 2002; U.S. Pat.No. 6,280,949 B1). In this technique, a random set of primers is used toprime a sample of genomic DNA. By selecting a sufficiently large set ofprimers of random or partially random sequence, the primers in the setwill be collectively, and randomly, complementary to nucleic acidsequences distributed throughout nucleic acids in the sample.Amplification proceeds by replication with a highly possessivepolymerase, ϕ29 DNA polymerase, initiating at each primer and continuinguntil spontaneous termination. Displacement of intervening primersduring replication by the polymerase allows multiple overlapping copiesof the entire genome to be synthesized.

The use of random primers to universally amplify genomic DNA is based onthe assumption that random primers equally prime over the entire genome,thus allowing representative amplification. Although the primersthemselves are random, the location of primer hybridization in thegenome is not random, as different primers have unique sequences andthus different characteristics (such as different melting temperatures).As random primers do not equally prime everywhere over the entiregenome, amplification is not completely representative of the startingmaterial. Such protocols are useful in studying specific loci, but theresult of random-primed amplification products is not representative ofthe starting material (e.g., the entire genome).

Cell Immortalization

Normal human somatic cells have a limited life span and enter senescenceafter a limited number of cell divisions (Hayflick and Moorhead, 1961;Hayflick 1965; Martin et al., 1970). At senescence, cells are viable butno longer divide. This limit on cell proliferation represents anobstacle to the study of normal human cells, especially since manyrounds of cell division are used, as cells are shared betweenlaboratories or to produce large quantities of cells required forbiochemical analysis, for genetic manipulations, or for genetic screens.This limitation is of particular concern for the study of rarehereditary human diseases, since the volume of the biological samplescollected (biopsies or blood) is usually small and contains a limitednumber of cells.

The establishment of permanent cell lines is one way to circumvent thislack of critical material. Some tumor cells yield cultures withunlimited growth potential, and in vitro transformation with oncogenesor carcinogens have proven a successful means to establish permanentfibroblast and lymphoblast cell lines. Such cell lines have beenvaluable in the analysis of mammalian biochemistry and theidentification of disease-related genes. However, such transformed cellstypically exhibit significant alterations in physiological andbiological properties. Most notably, these cells are associated withaneuploidy, spontaneous hypermutability, loss of contact inhibition andalterations in biochemical functions related to cell cycle checkpoints.These cellular properties that differ from their normal counterpartspose significant limitations to the analysis of many cellular functions,in particular those related to genomic integrity and the study of thehuman chromosome instability syndromes.

Recent advances have shown the onset of replicative senescence to becontrolled by the shortening of the telomeres that occurs each timenormal human cells divide (Allsopp et al., 1992; Allsopp et al., 1995;Bodnar et al., 1998; Vaziri and Benchimol, 1998). This loss of telomericDNA is a consequence of the inability of DNA polymerase alpha to fullyreplicate the ends of linear DNA molecules (Watson, 1972; Olovnikov,1973). It has been proposed that senescence is induced when the shortestone or two telomeres can no longer be protected by telomere-bindingproteins, and thus is recognized as a double-stranded (ds) DNA break. Incells with functional checkpoints, the introduction of dsDNA breaksleads to the activation of p53 and of the p16/pRB checkpoint and to agrowth arrest state that mimics senescence (Vaziri and Benchimol, 1996;Di Leonardo et al., 1994; Robles and Adami, 1998). Cell cycleprogression in senescent cells is also blocked by the same twomechanisms (Bond et al., 1996; Hara et al., 1996; Shay et al., 1991).This block can be overcome by viral oncogenes, such as SV40 large Tantigen, that can inactivate both p53 and pRB. Cells that express SV40large T antigen escape senescence but continue to lose telomeric repeatsduring their extended life span. These cells are not yet immortal, andterminal telomere shortening eventually causes the cells to reach asecond non-proliferative stage termed ‘crisis’ (Counter et al., 1992;Wright and Shay; 1992). Escape from crisis is a very rare event (1 in10⁷) usually accompanied by the reactivation of telomerase (Shay et al.,1993).

Telomerase is a specialized cellular reverse transcriptase that cancompensate for the erosion of telomeres by synthesizing new telomericDNA. The activity of telomerase is present in certain germline cells butis repressed during development in most somatic tissues, with theexception of proliferative descendants of stem cells such as those inthe skin, intestine and blood (Ulaner and Giudice, 1997; Wright et al.,1996; Yui et al., 1998; Ramirez et al., 1997; Hiyama et al., 1996). Theenzyme telomerase is a ribonuclear protein composed of at least twosubunits; an integral RNA, that serves as a template for the synthesisof telomeric repeats (hTR), and a protein (hTERT), that has reversetranscriptase activity. The RNA component (hTR) is ubiquitous in humancells, but the presence of the mRNA encoding hTERT is restricted to thecells with telomerase activity. The forced expression of exogenous hTERTin normal human cells is sufficient to produce telomerase activity inthese cells and prevent the erosion of telomeres and circumvent theinduction of both senescence and crisis (Bodnar et al., 1998; Vaziri andBenchimol, 1998). Recent studies have shown that telomerase canimmortalize a variety of cell types. Cells immortalized with hTERT havenormal cell cycle controls, functional p53 and pRB checkpoints, arecontact inhibited, are anchorage dependent, require growth factors forproliferation, and possess a normal karyotype (Morales et al., 1999;Jiang et at, 1999).

Thus, the related art provides a variety of techniques for whole genomeamplification, although there remains a need in the art for methods andcompositions amenable to non-biased highthroughput library generationand/or preparation of DNA molecules. For example, Japan Patent No.JP8173164A2 describes a method of preparing DNA by sorting-out PCR™amplification in the absence of cloning, fragmenting a double-strandedDNA, ligating a known-sequence oligomer to the cut end, and amplifyingthe resultant DNA fragment with a primer having the sorting-out sequencecomplementary to the oligomer. The sorting-out sequences consist of afluorescent label and one to four bases at the 5 and 3 termini toamplify the number of copies of the DNA fragment.

U.S. Pat. No. 6,107,023 describes a method of isolating duplex DNAfragments which are unique to one of two fragment mixtures, i.e.,fragments which are present in a mixture of duplex DNA fragments derivedfrom a positive source, but absent from a fragment mixture derived froma negative source. In practicing the method, double-strand linkers areattached to each of the fragment mixtures, and the number of fragmentsin each mixture is amplified by successively repeating the steps of (i)denaturing the fragments to produce single fragment strands; (ii)hybridizing the single strands with a primer whose sequence iscomplementary to the linker region at one end of each strand, to formstrand/primer complexes; and (iii) converting the strand/primercomplexes to double-stranded fragments in the presence of polymerase anddeoxynucleotides. After the desired fragment amplification is achieved,the two fragment mixtures are denatured, then hybridized underconditions in which the linker regions associated with the two mixturesdo not hybridize. DNA species unique to the positive-source mixture,i.e., which are not hybridized with DNA fragment strands from thenegative-source mixture, are then selectively isolated.

Patent WO/016545 A1 details a method for amplifying DNA or RNA using asingle primer for use as a fingerprinting method. This protocol wasdesigned for the analysis of microbial, bacterial and other complexgenomes that are present within samples obtained from organismscontaining even more complex genomes, such as animals and plants. Theadvantage of this procedure for amplifying targeted regions is thestructure and sequence of the primer. Specifically, the primer isdesigned to have very high cytosine and very low guanine content,resulting in a high melting temperature. Furthermore, the primer isdesigned in such a way as to have a negligible ability to form secondarystructure. This results in limited production of primer-dimer artifactsand improves amplification of regions of interest, without a prioriknowledge of these regions. In contrast to the current invention, thismethod is only able to prime a subset of regions within a genome, due tothe utilization of a single priming sequence. Furthermore, the structureof the primer contains only a constant priming region, as opposed to aconstant amplification region and a variable priming region in thepresent invention. Thus, a single primer consisting of non-degeneratesequence results in priming of a limited number of areas within thegenome, preventing amplification of the whole-genome.

U.S. Pat. No. 6,114,149 regards a method of amplifying a mixture ofdifferent-sequence DNA fragments that may be formed from RNAtranscription, or derived from genomic single- or double-stranded DNAfragments. The fragments are treated with terminal deoxynucleotidetransferase and a selected deoxynucleotide to form a homopolymer tail atthe 3′ end of the anti-sense strands, and the sense strands are providedwith a common 3′-end sequence. The fragments are mixed with ahomopolymer primer that is homologous to the homopolymer tail of theanti-sense strands, and a defined-sequence primer which is homologous tothe sense-strand common 3′-end sequence, with repeated cycles offragment denaturation, annealing, and polymerization, to amplify thefragments. In one embodiment, the defined-sequence and homopolymerprimers are the same, i.e., only one primer is used. The primers maycontain selected restriction-site sequences to provide directionalrestriction sites at the ends of the amplified fragments.

U.S. Pat. Nos. 6,124,120 and 6,280,949 describe compositions and amethod for amplification of nucleic acid sequences based on multiplestrand displacement amplification (MSDA). Amplification takes place notin cycles, but in a continuous, isothermal replication. Two sets ofprimers are used, a right set and a left set complementary to nucleotidesequences flanking the target nucleotide sequence. Amplificationproceeds by replication initiated at each primer and continuationthrough the target nucleic acid sequence through displacement ofintervening primers during replication. This allows multiple copies of anested set of the target nucleic acid sequence to be synthesized in ashort period of time. In another form of the method, referred to aswhole genome strand displacement amplification (WGSDA), a random set ofprimers is used to randomly prime a sample of genomic nucleic acid. Inan alternative embodiment, referred to as multiple strand displacementamplification of concatenated DNA (MSDA-CD), fragments of DNA are firstconcatenated together with linkers. The concatenated DNA is thenamplified by strand displacement synthesis with appropriate primers. Arandom set of primers can be used to randomly prime synthesis of the DNAconcatemers in a manner similar to whole genome amplification. Primerscomplementary to linker sequences can be used to amplify theconcatemers. Synthesis proceeds from the linkers through a section ofthe concatenated DNA to the next linker, and continues beyond. As thelinker regions are replicated, new priming sites for DNA synthesis arecreated. In this way, multiple overlapping copies of the entireconcatenated DNA sample can be synthesized in a short time.

U.S. Pat. No. 6,365,375 describes a method for primer extensionpre-amplification of DNA with completely random primers in apre-amplification reaction, and locus-specific primers in a secondamplification reaction using two thermostable DNA polymerases, one ofwhich possesses 3″-5″ exonuclease activity. Pre-amplification isperformed by 20 to 60 thermal cycles. The method uses a slow transitionbetween the annealing phase and the elongation phase. Two elongationsteps are performed: one at a lower temperature and a second at a highertemperature. Using this approach, populations of especially longamplicons are claimed. The specific primers used in the secondamplification reaction are identical to a sequence of the target nucleicacid or its complementary sequence. Specific primers used to carry out anested PCR in a potential third amplification reaction are selectedaccording to the same criteria as the primers used in the secondamplification reaction. A claimed advantage of the method is itsimproved sensitivity to the level of a few cells and increased fidelityof the amplification due to the presence of proof-reading 3′-5′exonuclease activity, as compared to methods using only one thermostableDNA polymerase, i.e. Taq polymerase.

Bohlander et al. (1992) have developed a method by which microdissectedmaterial can be amplified in two initial rounds of DNA synthesis with T7DNA polymerase using a primer that contains a random five base sequenceat its 3′ end and a defined sequence at its 5′ end. The pre-amplifiedmaterial is then further amplified by PCR using a second primerequivalent to the constant 5′ sequence of the first primer.

Using modification of Bohlander's procedure and DOP-PCR, Guan et al.(1993) were able to increase sensitivity of amplification ofmicrodissected chromosomes using DOP-PCR primers in a cyclingpre-amplification reaction with Sequenase version 2 (replenished aftereach denaturing step by fresh enzyme) followed by PCR amplification withTaq polymerase.

Another modification of the original Bohlander's method has beenpublished in a collection of protocols for DNA preparation in microarrayanalysis on the World Wide Web by the Department of Biochemistry andBiophysics at the University of California at San Francisco. Thisprotocol has been used to amplify genomic representations of less than 1ng of DNA. The protocol consists of three sets of enzymatic reactions.In Round A, Sequenase is used to extend primers containing a completelyrandom sequence at its 3′ end and a defined sequence at its 5′ end togenerate templates for subsequent PCR. During Round B, the specificprimer B is used to amplify the templates previously generated. Finally,Round C consists of additional PCR cycles to incorporate either aminoallyl dUTP or cyanine modified nucleotides.

Zheleznaya et al. (1999) developed a method to prepare random DNAfragments in which two cycles are performed with Klenow fragment of DNApolymerase I and primers with random 3′-sequences and a 5′-constant partcontaining a restriction site. After the first cycle, the DNA isdenatured and new Klenow fragment is added. Routine PCR amplification isthen performed utilizing the constant primer.

In contrast to other methods in the art, the present invention providesa variety of new ways of preparing DNA templates, particularly for wholegenome amplification, and preferentially in a manner representative of anative genome.

RNA Expression Analysis

The expression of genes and regulatory transcripts encoded within DNA isthe primary mechanism regulating cellular metabolism. Transcription andthe post-transcriptional processing of RNA sets the framework for allphases of cellular function. For proteins that control essentialcellular functions, such as replication and differentiation, the levelsof RNA expression and protein synthesis are tightly correlated. Changeswithin the environment of a cell or tissue often result in necessaryalterations in cellular functions. For example, a cell may alter thepattern of gene expression in response to environmental factors, such asligand and metabolite stimulated signaling. Furthermore, cellularexpression of RNA and proteins may be altered intentionally as with theuse of some therapeutic drugs. These changes in gene expression may bedue to both the beneficial and the toxic effects of these drugs.Alterations in gene expression in both the normal or diseased state canbe utilized for determining the efficacy and mechanisms of action ofpotential treatments. In the case of oncogenic transformation, cells mayexhibit subtle changes in expression during cancer progression. Changesin gene expression of key proteins involved in cellular transformationhave the potential to be used as predictive markers of oncogenesis. Thesequencing and mapping of the human genome has resulted in a database ofpotentially expressed genes. Several tools, including high-densitymicro-arrays have been developed to measure the expression of each ofthese genes, including potential splice variants.

Transcribed genes at any given moment in the life of a cell or tissuerepresent the regulatory and protein-coding responses involved incellular function. In some embodiments, the present invention relates tothe unbiased amplification of sequences representative of the RNAprofile. High fidelity amplification of expressed genes from localizedtissues, small groups of cells, or a single cell, will allow theanalysis of subtle alterations in gene expression. The need to profile awide range of potentially expressed RNA molecules from limited samplematerial requires an amplification method that maintains therepresentation of the starting material. The invention described hereinprovides a method to produce a large amount of cDNA from amounts of RNAtypically recovered in clinical and diagnostic applications that are notsufficient for direct processing. Whole transcriptome amplification hasa relatively brief history with methods based primarily on quasi-linearamplification and exponential amplification.

Both transcription based and PCR based methods for amplification of RNAsequences rely on the activity of RNA dependent DNA polymerases such asthe various reverse transcriptases of viral origin. It can be arguedthat regardless of the priming and amplification strategy, sequencespecific bias for reverse transcription is unavoidable. This source ofbias is addressed in gene profiling experiments by drawing comparisonsbetween similarly amplified control and test samples.

Linear transcription based and single primer amplification (SPA) basedmethods require an initial reverse transcription step using eitherrandom or poly-T priming. To facilitate amplification of the resultingcDNA, primers utilized for reverse transcription may contain anon-complementary tail introducing a specific universal sequence. In thecase of in vitro transcription (IVT) based amplification methods,specific binding and initiation sites are introduced as 5′ oligoextensions corresponding to one of the phage RNA polymerase priming andrecognition sites (Phillips and Eberwine, 1996; U.S. Ser. No.00/551,4545A). RNA/DNA duplexes resulting from reverse transcription orfirst strand cDNA synthesis serve as the template for second strand cDNAsynthesis after degradation of the RNA strand by RNase H. Second strandcDNA products may be primed randomly or terminally to incorporate theRNA polymerase recognition sites in the tailed primers, therebygenerating substrate for linear amplification. Various modifications tothe protocol include second strand priming utilizing terminaltransferase to extend first strand cDNA products to introduce shortstretches of guanine (Wang and Chung; U.S. Ser. No. 00/593,2451A), andutilizing the native terminal transferase activity of Moloney murineleukemia virus reverse transcriptase, which has the propensity to addthree to five cytosine ribonucleotides to the 3′ terminus of extensionproducts. This activity has been used for second strand priming byGinsberg and Che (US20030186237A1), and in the “SMART” adaptation(Clontech), wherein a strand-switching adapter is employed, having aseries of guanine residues at its 3′ end which can prime the extendedpoly-C tail (Schmidt et al., 1999).

An alternative to linear amplification by RNA polymerase is “SinglePrimer Amplification” (SPA), whereby the initial reverse transcriptaseincorporated primer sequence designates the binding site for primerannealing in sequential rounds of primer extension with Taq polymerase(Smith et al., 2003). In a specialized version of SPA the reaction iscarried out under isothermal conditions whereby the primer consistspartially of DNA and partially of RNA. In the presense of standdisplacing polymerase activity and RNase H activity, each primerextension product generates substrate for RNase H within the 5′ RNAcomponent of the primer. Cleavage of the extension products generatessuccessive priming sites, and the reaction cycles in a linear stranddisplacement isothermal mode. (NuGEN Technologies Inc.; WO 02/72772;US2003/0017591 A1; US2003/0017591 A1). Sequential rounds oftranscription and reverse transcription are capable of producing as muchas a million fold amplification.

PCR based amplification of RNA involves the same initial steps ofreverse transcription and second strand synthesis. While those familiarwith the art will appreciate the potential to introduce bias uponexponential amplification, several methods have demonstrated theamplified products to have minimal distortion and be highlyrepresentative of the original RNA transcripts. The standard methodemploys double stranded cDNA generated by classical first and secondstrand synthesis. Briefly, reverse transcriptase initiates from oligo dTand random primers to promote first strand synthesis followed by acocktail of DNA polymerase I, RNase H and DNA ligase for second strandsynthesis and repair. Universal adaptors, containing a known sequence,can then be ligated to the double strand cDNA molecules for subsequentamplification. This process can be substantially improved by avoidingthe requirement for ligation mediated adapter ligation through the useof a reverse transcriptase non-template directed addition of cytosineresidues. A universal sequence is subsequently introduced as a primerfor strand switching mediated second strand cDNA synthesis (Schmidt etal., 1999).

Further improvements aimed at neutralizing bias introduced betweensamples have been demonstrated using modified primers that contain bothuniversal and unique priming sites. Makrigiorgos et al. (2002)demonstrated the utility of “balanced PCR” using a bipartite primerconstruction to co-amplify multiple samples that share a common distalprimer sequence. The mixture of samples can be co-amplified, minimizingeffects of any impurities or other factors affecting the amplification.The pooled samples are subsequently separated based on the individualsequence tags, from their respective proximal primer sequence, in eithera secondary low cycle amplification or a primer extension labelingreaction.

Although exponential amplification has the reputation of degrading therelative abundance relationships between transcripts, much of the biascan be attributed to the various steps required in generating theamplimers. The specific sequence of any given transcript may affect theefficiency of reverse transcription, and these effects may beexaggerated as the length of the transcript increases. Methods employingcombinations of IVT-based and PCR-based amplification provide both asensitive and a specific approach, although they retain an intermediatestepwise synthesis of first and second strand cDNA (RosettaInpharmatics, Inc. U.S. Ser. No. 00/627,1002B1; Roche Diagnostics Co.US20030113754A1).

The present invention minimizes the introduction of bias by capturingtranscripts, in a single step, in the form of amplimers with a uniformsize distribution. WTA products are synthesized independent of theintegrity of the RNA molecule, the ability to complete reversetranscription of the entire RNA molecule, the requirement for templateswitching during second strand synthesis, and the ligation of adapters.Subsequent amplification of the products using a universalnon-self-complementary primer results in unbiased representationsuitable for all applications, such as downstream expression studies.

SUMMARY OF THE INVENTION

The present invention regards the amplification of a whole genome, orwhole transcriptome, including various methods and compositions toachieve that goal. In specific embodiments, a whole genome is amplifiedfrom a single cell, whereas in another embodiment the whole genome isamplified from a plurality of cells. In specific embodiments the wholetranscriptome is amplified from poly A+ RNA, or in another embodimentthe whole transcriptome is amplified from total RNA.

In a particular aspect of the present invention, the invention isdirected to methods for the amplification of substantially the entiregenome or entire transcriptome without loss of representation ofspecific sites (herein defined as “whole genome amplification” and“whole transcriptome amplification”, respectively). In a specificembodiment, whole genome amplification comprises simultaneousamplification of substantially all fragments of a genomic library. In afurther specific embodiment, “substantially entire” or “substantiallyall” refers to about 80%, about 85%, about 90%, about 95%, about 97%, orabout 99% of all sequence in a genome. A skilled artisan recognizes thatamplification of the whole genome will, in some embodiments, comprisenon-equivalent amplification of particular sequences over others,although the relative difference in such amplification is notconsiderable.

In specific embodiments, the present invention regards immortalizationof DNA following generation of a library comprising a representativeamplifiable copy of the template DNA. The library generation steputilizes special self-inert degenerate primers designed to eliminatetheir ability to form primer-dimers and a polymerase comprisingstrand-displacement activity.

In one particular aspect of the present invention, there is a method foruniform amplification of DNA or RNA using self-inert degenerate primerscomprised essentially of non-self-complementary nucleotides. In specificembodiments, the degenerate oligonucleotides do not participate inWatson-Crick base-pairing with one another. This lack of primercomplementarity overcomes major problems known in the art associatedwith DNA amplification by random primers, such as excessive primer-dimerformation, complete or sporadic locus dropout, generation of very shortamplification products, and in some cases the inability to amplifysingle stranded, short, or fragmented DNA and RNA molecules.

In specific embodiments, the invention provides a two-step procedurethat can be performed in a single tube or in a micro-titer plate, forexample, in a high throughput format. The first step (termed the“library synthesis step”) involves incorporation of known sequence atboth ends of amplicons using highly degenerate primers and at least oneenzyme possessing strand-displacement activity. The resulting branchingprocess creates molecules having self-complementary ends. The resultinglibrary of molecules are then amplified in a second step by PCR™ using,for example, Taq polymerase and a primer corresponding to the knownsequence, resulting in several thousand-fold amplification of the entiregenome or transcriptome without significant bias. The products of thisamplification can be re-amplified additional times, resulting inamplification that exceeds, for example, several million fold.

Thus, in one particular aspect of the present invention, there is amethod of preparing a nucleic acid molecule, comprising obtaining atleast one single stranded nucleic acid molecule; subjecting said singlestranded nucleic acid molecule to a plurality of primers to form asingle stranded nucleic acid molecule/primer mixture, wherein theprimers comprise nucleic acid sequence that is substantiallynon-self-complementary and substantially non-complementary to otherprimers in the plurality, wherein said sequence comprises in a 5′ to 3′orientation a constant region and a variable region; and subjecting saidsingle stranded nucleic acid molecule/primer mixture to astrand-displacing polymerase, under conditions wherein said subjectingsteps generate a plurality of molecules including all or part of theknown nucleic acid sequence at each end. In a specific aspect, themethod is further defined as comprising: (1) a first series ofpolymerase chain reaction steps comprising subjecting the nucleic acidmolecule/primer mixture to a thermostable polymerase in the presence ofthe primers; and (2) a second series of polymerase chain reaction stepsusing primers that comprise the constant region and under temperaturesno less than about 60° C. (wherein about 60° C. may include 57° C., 58°C., or 59° C.

The method may further comprise the step of designing the primers suchthat they purposefully are substantially non-self-complementary andsubstantially noncomplementary to other primers in the plurality. Themethod may also further comprise the step of amplifying a plurality ofthe molecules comprising the known nucleic acid sequence to produceamplified molecules. Such amplification may comprise polymerase chainreaction, such as that utilizes a primer complementary to the knownnucleic acid sequence.

The primers may comprise a constant region and a variable region, bothof which include nucleic acid sequence that is substantiallynon-self-complementary and substantially non-complementary to otherprimers in the plurality. In specific embodiments, the constant regionand variable region for a particular primer are comprised of the sametwo nucleotides, although the sequence of the two regions are usuallydifferent. The constant region is preferably known and may be a targetedsequence for a primer in amplification methods. The variable region mayor may not be known, but in preferred embodiments is known. The variableregion may be randomly selected or may be purposefully selectedcommensurate with the frequency of its representation in a source DNA,such as genomic DNA. In specific embodiments, the nucleotides of thevariable region will prime at target sites in a source DNA, such as agenomic DNA, containing the corresponding Watson-Crick base partners. Ina particular embodiment, the variable region is considered degenerate.

The single stranded nucleic acid molecule may be DNA, in someembodiments, and in alternative embodiments the single stranded nucleicacid molecule is RNA or a DNA-RNA chimera.

In other aspects of the invention, a tag is incorporated on the ends ofthe amplified molecules, preferably wherein the known sequence ispenultimate to the tags on each end of the amplified molecules. The tagmay be a homopolymeric sequence, in specific embodiments, such as apurine. The homopolymeric sequence may be single stranded, such as asingle stranded poly G or poly C. Also, the homopolymeric sequence mayrefer to a region of double stranded DNA wherein one strand ofhomopolymeric sequence comprises all of the same nucleotide, such aspoly C, and the opposite strand of the double stranded regioncomplementary thereto comprises the appropriate poly G.

The incorporation of the homopolymeric sequence may occur in a varietyof ways known in the art. For example, the incorporation may compriseterminal deoxynucleotidyl transferase activity, wherein a homopolymerictail is added via the terminal deoxynucleotidyl transferase enzyme.Other enzymes having analogous activities may be utilized, also. Theincorporation of the homopolymeric sequence may comprise ligation of anadaptor comprising the homopolymeric sequence to the ends of theamplified molecules. An additional example of incorporation of thehomopolymeric sequence employs replicating the amplified molecules withDNA polymerase by utilizing a primer comprising in a 5′ to 3′orientation, the homopolymeric sequence, and the known sequence.

In additional embodiments of the present invention, the amplifiedmolecules comprising the homopolymeric sequence are further amplifiedusing a primer complementary to a known sequence and a primercomplementary to the homopolymeric sequence. The present inventors havedemonstrated that when the molecules comprise a guanine homopolymericsequence, for example, surprisingly, the amplification of molecules withjust the homo-cytosine primer is suppressed in favor of amplification ofmolecules with the primer complementary to a specific sequence (such asthe known sequence) and the homo-cytosine primer. These embodiments maybe utilized, for example, in the scenario wherein a small amount of DNAis available for processing, and it is converted into a library,amplified using universal primer, and then re-amplified or replicatedwith a new universal primer that has the same universal sequence at the3′ end plus a homopolymeric (such as poly C) stretch at the 5′ end. Thismay then be used as an unlimited resource for targetedamplification/sequencing, for example, in specific embodiments.

In specific embodiments of the present invention, the obtaining step maybe further defined as comprising the steps of obtaining at least onedouble stranded DNA molecule and subjecting the double stranded DNAmolecule to heat to produce at least one single stranded DNA molecule.

Nucleic acids processed by methods described herein may be DNA, RNA, orDNA-RNA chimeras, and they may be obtained from any useful source, suchas, for example, a human sample. In specific embodiments, a doublestranded DNA molecule is further defined as comprising a genome, suchas, for example, one obtained from a sample from a human. The sample maybe any sample from a human, such as blood, serum, plasma, cerebrospinalfluid, cheek scrapings, nipple aspirate, biopsy, semen (which may bereferred to as ejaculate), urine, feces, hair follicle, saliva, sweat,immunoprecipitated or physically isolated chromatin, and so forth. Inspecific embodiments, the sample comprises a single cell.

In particular embodiments of the present invention, the prepared nucleicacid molecule from the sample provides diagnostic or prognosticinformation. For example, the prepared nucleic acid molecule from thesample may provide genomic copy number and/or sequence information,allelic variation information, cancer diagnosis, prenatal diagnosis,paternity information, disease diagnosis, detection, monitoring, and/ortreatment information, sequence information, and so forth.

In particular aspects of the present invention, the primers are furtherdefined as having a constant first and variable second regions eachcomprised of two non-complementary nucleotides. The first and secondregions may be each comprised of guanines, adenines, or both; ofcytosines, thymidines, or both; of adenines, cytosines, or both; or ofguanines, thymidines, or both. The first region may comprise about 6 toabout 100 nucleotides. The second region may comprise about 4nucleotides to about 20 nucleotides. The polynucleotide (primer) may befurther comprised of 0 to about 3 random bases at its distal 3′ end. Inparticular embodiments, the nucleotides are base or backbone analogs.

In particular embodiments, the first region and the second region areeach comprised of guanines and thymidines and the polynucleotide(primer) comprises about 1, 2, or 3 random bases at its 3′ end, althoughit may comprise 0 random bases at its 3′ end.

The known nucleic acid sequence may be used for subsequentamplification, such as with polymerase chain reaction.

In some embodiments, methods of the present invention utilize astrand-displacing polymerase, such as D29 Polymerase, Bst Polymerase,Vent Polymerase, 9° Nm Polymerase, Klenow fragment of DNA Polymerase I,MMLV Reverse Transcriptase, AMV reverse transcriptase, HIV reversetranscriptase, a mutant form of T7 phage DNA polymerase that lacks 3′-5′exonuclease activity, or a mixture thereof. In a specific embodiment,the strand-displacing polymerase is Klenow or is the mutant form of T7phage DNA polymerase that lacks 3′→5′ exonuclease activity.

Methods utilized herein may further comprise subjecting single strandednucleic acid molecule/primer mixtures to a polymerase-processivityenhancing compound, such as, for example, single-stranded DNA bindingprotein or helicase.

In some embodiments of the present invention, there is a method ofamplifying at least one RNA molecule, comprising obtaining an RNAmolecule; subjecting the RNA molecule to a plurality of primers to forma RNA molecule/primer mixture, wherein the primers comprise nucleic acidsequence that is substantially non-self-complementary and substantiallynon-complementary to other primers in the plurality, wherein thesequence comprises in a 5′ to 3′ orientation a constant region and avariable region; subjecting the RNA molecule/primer mixture to apolymerase, under conditions wherein the subjecting steps generate aplurality of DNA molecules comprising the constant region at each end;and amplifying a plurality of the DNA molecules through polymerase chainreaction, said reaction utilizing a primer complementary to the constantregion.

The RNA molecule may be obtained from a sample, such as a samplecomprising total cellular RNA, a transcriptome, or both; the sample maybe obtained from one or more viruses; from one or more bacteria; or froma mixture of animal cells, bacteria, and/or viruses, for example. Thesample may comprise mRNA, such as mRNA that is obtained by affinitycapture

In another aspect of the present invention, there is a method ofamplifying a genome, transcriptome, or both comprising obtaining genomicDNA, RNA (such as mRNA) or both; modifying the genomic DNA, RNA, or bothto generate at least one single stranded nucleic acid molecule;subjecting said single stranded nucleic acid molecule to a plurality ofprimers to form a nucleic acid/primer mixture, wherein the primerscomprise nucleic acid sequence that is substantiallynon-self-complementary and substantially non-complementary to otherprimers in the plurality, wherein said sequence comprises in a 5′ to 3′orientation a constant region and a variable region; subjecting saidnucleic acid/primer mixture to a strand-displacing polymerase, underconditions wherein said subjecting steps generate a plurality of DNAmolecules comprising the constant region at each end; and amplifying aplurality of the DNA molecules through polymerase chain reaction, saidreaction utilizing a primer complementary to the constant nucleic acidsequence.

The method may further comprise the steps of modifying double strandedDNA molecules to produce single stranded molecules, said single strandedmolecules comprising the known nucleic acid sequence at both the 5′ and3′ ends; hybridizing a region of at least one of the single stranded DNAmolecules to a complementary region in the 3′ end of an oligonucleotideimmobilized to a support to produce a single strandedDNA/oligonucleotide hybrid; and extending the 3′ end of theoligonucleotide to produce an extended polynucleotide. In specificembodiments, the method further comprises the step of removing thesingle stranded DNA molecule from the single strandedDNA/oligonucleotide hybrid.

In one aspect of the invention, there is a method of obtaining a totalnucleic acid from a sample comprising a mixture of DNA and RNA,comprising providing the mixture of DNA and RNA; optionally heating themixture to a temperature that denatures double stranded nucleic acids;and subjecting the mixture to a polymerase that replicates both singlestranded DNA and RNA. In some embodiments, the method consistsessentially of said providing, optionally heating, and subjecting steps.The subjecting step may be further defined as subjecting the mixture toa plurality of primers to form a nucleic acid/primer mixture, whereinthe primers comprise nucleic acid sequence that is substantiallynon-self-complementary and substantially non-complementary to otherprimers in the plurality, wherein said sequence comprises in a 5′ to 3′orientation a constant region and a variable region; subjecting saidnucleic acid/primer mixture to the polymerase that efficientlyreplicates both DNA and RNA, under conditions wherein said subjectingsteps generate a plurality of DNA molecules comprising the constantnucleic acid sequence at each end; and amplifying a plurality of the DNAmolecules comprising the constant region at each end through polymerasechain reaction, said reaction utilizing a primer complementary to theconstant region.

In another aspect of the present invention, there is a method ofamplifying a total transcriptome, comprising obtaining total RNA;subjecting said RNA molecule to a plurality of primers to form anRNA/primer mixture, wherein the primers comprise nucleic acid sequencethat is substantially non-self-complementary and substantiallynon-complementary to other primers in the plurality, wherein saidsequence comprises in a 5′ to 3′ orientation a constant region and avariable region; subjecting said RNA/primer mixture to a reversetranscriptase, under conditions wherein said subjecting steps generate aplurality of DNA molecules comprising the constant region at each end;and amplifying a plurality of the DNA molecules through polymerase chainreaction, said reaction utilizing a primer complementary to the knownnucleic acid sequence.

In another aspect of the present invention, there is a method ofamplifying a protein-coding transcriptome, comprising obtaining mRNA;subjecting the mRNA molecule to a plurality of primers to form anmRNA/primer mixture, wherein the primers comprise nucleic acid sequencethat is substantially non-self-complementary and substantiallynon-complementary to other primers in the plurality, wherein saidsequence comprises in a 5′ to 3′ orientation a constant region and avariable region; subjecting said mRNA/primer mixture to a reversetranscriptase, under conditions wherein said subjecting steps generate aplurality of DNA molecules comprising the constant region at each end;and amplifying a plurality of the DNA molecules through polymerase chainreaction, said reaction utilizing a primer complementary to the constantregion.

In other aspects of the present invention, there is a method ofamplifying a DNA molecule generated from at least one mRNA molecule,comprising obtaining a cDNA molecule from the mRNA molecule; modifyingthe cDNA molecule to generate at least one ssDNA molecule; subjectingthe ssDNA molecule to a plurality of primers to form a ssDNAmolecule/primer mixture, wherein the primers comprise nucleic acidsequence that is substantially non-self-complementary and substantiallynon-complementary to other primers in the plurality, wherein thesequence comprises, in a 5′ to 3′ orientation, a constant region and avariable region; subjecting the ssDNA molecule/primer mixture to astrand-displacing polymerase, under conditions wherein the subjectingsteps generate a plurality of DNA molecules comprising the constantregion at each end; and amplifying a plurality of the DNA moleculescomprising the constant region at each end through polymerase chainreaction, said reaction utilizing a primer complementary to the constantregion.

The obtaining step may be further defined as comprising generation ofthe cDNA molecule by reverse transcribing the mRNA molecule with areverse transcriptase, such as, for example Tth DNA polymerase, HIVReverse Transcriptase, AMV Reverse Transcriptase, MMLV ReverseTranscriptase, or a mixture thereof.

In another aspect of the present invention, there is a kit comprising aplurality of polynucleotides, wherein the polynucleotides comprisenucleic acid sequence that is substantially non-self-complementary andsubstantially non-complementary to other polynucleotides in theplurality, said plurality dispersed in a suitable container. The kit mayfurther comprise a polymerase, such as a strand displacing polymerase,including, for example, 029 Polymerase, Bst Polymerase, Vent Polymerase,9° Nm Polymerase, Klenow fragment of DNA Polymerase I, MMLV ReverseTranscriptase, a mutant form of T7 phage DNA polymerase that lacks 3′-5′exonuclease activity, or a mixture thereof.

In an additional aspect of the invention, there is a method ofamplifying a population of DNA molecules comprised in a plurality ofpopulations of DNA molecules, said method comprising the steps ofobtaining a plurality of populations of DNA molecules, wherein at leastone population in said plurality comprises DNA molecules having in a 5′to 3′ orientation a known identification sequence specific for thepopulation and a known primer amplification sequence; and amplifying thepopulation of DNA molecules by polymerase chain reaction, the reactionutilizing a primer for the identification sequence.

The obtaining step may be further defined as obtaining a population ofDNA molecules comprising a known primer amplification sequence;amplifying said DNA molecules with a primer having in a 5′ to 3′orientation the known identification sequence and the known primeramplification sequence, and mixing the population with at least oneother population of DNA molecules. In specific embodiments, thepopulation of DNA molecules comprises genomic DNA, is a genome, or is atranscriptome.

In another aspect of the present invention, there is a method ofamplifying a population of DNA molecules comprised in a plurality ofpopulations of DNA molecules by obtaining a plurality of populations ofDNA molecules, wherein at least one population in the pluralitycomprises DNA molecules, wherein the 5′ ends of the DNA moleculescomprise in a 5′ to 3′ orientation a single-stranded region comprising aknown identification sequence specific for the population and a knownprimer amplification sequence; isolating the population through bindingof at least part of the single stranded known identification sequence ofa plurality of the DNA molecules to a surface; and amplifying theisolated DNA molecules by polymerase chain reaction that utilizes aprimer complementary to the primer amplification sequence.

The obtaining step may be further defined as obtaining a population ofDNA molecules comprising a known primer amplification sequence;amplifying the DNA molecules with a primer comprising in a 5′ to 3′orientation: the known identification sequence; a non-replicable linker;and the known primer amplification sequence; and mixing the populationwith at least one other population of DNA molecules. Furthermore, theisolating step may be further defined as binding at least part of thesingle stranded known identification sequence to an immobilizedoligonucleotide comprising a region complementary to the knownidentification sequence.

In other aspects of the invention, there is a plurality ofpolynucleotides, wherein the polynucleotides in the plurality comprisenucleic acid sequence that is substantially non-self-complementary andsubstantially non-complementary to other polynucleotides in theplurality. The nucleic acid sequence may be further defined as renderingthe polynucleotides substantially incapable of at least one of thefollowing self-hybridization; self-priming; hybridization to anotherpolynucleotide in the plurality; and initiation of a polymerizationreaction in the plurality. The polynucleotides in the plurality may befurther defined as having a 5′ to 3′ orientation and comprising aconstant first region 5′ to a variable second region. In specificembodiments, the constant region is for subsequent amplification and/orthe variable region is for random annealing, random priming, or both.

The first and second regions of the polynucleotides may each becomprised of two non-complementary nucleotides, such as guanines,adenines, or both; cytosines, thymidines, or both; adenines, cytosines,or both; or guanines, thymidines, or both. The first region may compriseabout 6 to about 100 nucleotides and/or the second region may compriseabout 4 nucleotides to about 20 nucleotides. Furthermore, thepolynucleotide may further comprise 0 to about 3 random bases at itsdistal 3′ end. The nucleic acid sequence may be comprised of base orbackbone analogs, or both, in some embodiments.

In a particular embodiment, the first region and the second region areeach comprised of guanines and thymidines and the polynucleotidecomprises 0, 1, 2, or 3 random bases at its 3′ end.

In some embodiments, there is a method of differentially obtaining RNAfrom a sample comprising dsDNA and RNA, comprising providing the mixtureof dsDNA and RNA; optionally heating said mixture to a temperature notexceeding about 75° C. to prevent denaturation of dsDNA; and subjectingthe mixture to a polymerase that replicates only single stranded RNAtemplates. In specific embodiments, the method consists essentially ofthe providing and subjecting steps, or of the providing, optionallyheating, and subjecting steps. The subjecting step is further defined assubjecting the mixture to a plurality of primers to form assRNA/dsDNA/primer mixture, wherein the primers comprise nucleic acidsequence that is substantially non-self-complementary and substantiallynon-complementary to other primers in the plurality, wherein saidsequence comprises in a 5′ to 3′ orientation a constant region and avariable region; subjecting said ssRNA/dsDNA/primer mixture to apolymerase that prime and replicate only single-stranded RNA, underconditions wherein said subjecting steps generate a plurality of DNAmolecules comprising the constant nucleic acid sequence at each end; andamplifying a plurality of the DNA molecules comprising the constantregion at each end through polymerase chain reaction, said reactionutilizing a primer complementary to the constant region.

In another aspect of the present invention, there is a method ofimmobilizing an amplified genome, transcriptome, or both, by obtainingan amplified genome, transcriptome, or both, wherein a plurality ofmolecules from the genome, transcriptome, or both comprise a knownprimer amplification sequence at both the 5′ and 3′ ends of themolecules; and attaching a plurality of the molecules to a support. Theattaching step may be further defined as comprising covalently attachingthe plurality of molecules to the support through said known primeramplification sequence.

In specific embodiments, the covalently attaching step is furtherdefined as hybridizing a region of at least one single stranded moleculeto a complementary region in the 3′ end of a oligonucleotide immobilizedto said support; and extending the 3′ end of the oligonucleotide toproduce a single stranded molecule/extended polynucleotide hybrid. Themethod may also further comprise the step of removing the singlestranded molecule from the single stranded molecule/extendedpolynucleotide hybrid to produce an extended polynucleotide. The methodmay also further comprise the step of replicating the extendedpolynucleotide. The replicating step may be further defined as providingto said extended polynucleotide a polymerase and a primer complementaryto the known primer amplification sequence; extending the 3′ end of saidprimer to form an extended primer molecule; and releasing said extendedprimer molecule.

In another particular aspect of the invention, there is a method ofimmobilizing an amplified genome, comprising the steps of obtaining anamplified genome, wherein a plurality of DNA molecules from the genomeand comprise a tag; and a known primer amplification sequence at boththe 5′ and 3′ ends of the molecules; and attaching a plurality of theDNA molecules to a support. In a specific embodiment, the attaching stepis further defined as comprising attaching the plurality of DNAmolecules to the support through said tag. The tag may be biotin and thesupport may comprise streptavidin. In specific embodiments, the tagcomprises an amino group or a carboxy group, for example, although othertags useful in the art are contemplated.

However, in a particular aspect of the invention, the tag comprises asingle stranded region and the support comprises an oligonucleotidecomprising a sequence complementary to a region of the tag. The tag maycomprise a single stranded region further defined as an identificationsequence. Furthermore, the DNA molecules may be further defined ascomprising a non-replicable linker that is 3′ to the identificationsequence and that is 5′ to the known primer amplification sequence. In aspecific embodiment, the method further comprises the steps of removingcontaminants from the immobilized genome.

Methods having amplified molecules may further comprise the steps ofmodifying the amplified molecules, the molecules further defined asdouble stranded molecules, to incorporate modified nucleotide bases,thereby producing labeled molecules; generating single strandedmolecules from the labeled molecules, the single stranded moleculescapable of hybridizing to complementary sequences arrayed in knownlocations on a substrate; and analyzing at least one hybridizationsignal. The modifying step may comprise chemical, enzymatic, or physicalincorporation of modified nucleotide bases, which, for example, areradioactive or fluorescent. In specific embodiments, the generating stepcomprises denaturation of the double stranded molecules. The substratemay comprise a microarray substrate. Furthermore, the analyzing step maycomprise measuring the background subtracted intensity of the at leastone hybridization signal and/or measuring copy number, representation,or both of the amplified molecules.

In an additional embodiment of the present invention, there is a methodof differentially obtaining DNA or RNA, respectively, from a samplecomprising a mixture of DNA and RNA, comprising providing the mixture ofDNA and RNA; heating the mixture to a temperature that selectivelyaffects the DNA or RNA; subjecting the mixture to a polymerase thatselectively replicates the respective DNA or RNA. The subjecting stepmay be further defined as subjecting the mixture to a plurality ofprimers to form a ssDNA/RNA/primer mixture, wherein the primers comprisenucleic acid sequence that is substantially non-self-complementary andsubstantially non-complementary to other primers in the plurality,wherein said sequence comprises in a 5′ to 3′ orientation a constantregion and a variable region; subjecting said ssDNA/RNA/primer mixtureto the polymerase that selectively replicates the respective DNA or RNA,under conditions wherein said subjecting steps generate a plurality ofDNA molecules comprising the constant region at each end; and amplifyinga plurality of the DNA molecules comprising the constant region at eachend through polymerase chain reaction that utilizes a primercomplementary to the constant region.

In certain aspects, there is a method of differentially obtaining DNAfrom a sample comprising DNA and RNA, comprising providing the mixtureof DNA and RNA; heating said mixture to a temperature of at least about94° C. to about 100° C. to generate single stranded nucleic acids; andsubjecting the mixture to a polymerase that replicates only DNAtemplates. The method may further comprise subjecting the mixture to aplurality of primers to form a ssDNA/RNA/primer mixture, wherein theprimers comprise nucleic acid sequence that is substantiallynon-self-complementary and substantially non-complementary to otherprimers in the plurality, wherein said sequence comprises in a 5′ to 3′orientation a constant region and a variable region; and subjecting saidssDNA/RNA/primer mixture to a polymerase that selectively replicatesDNA, under conditions wherein the subjecting steps generate a pluralityof DNA molecules comprising the known nucleic acid sequence at each end.The method may further comprise the step of amplifying a plurality ofthe DNA molecules through polymerase chain reaction, said reactionutilizing a primer complementary to the constant region. The polymerasemay be a DNA-dependent DNA polymerase, in specific embodiments, such asϕ29 Polymerase, Bst Polymerase, Vent Polymerase, 9° Nm Polymerase,Klenow Exo⁻ fragment of DNA Polymerase I, a mutant form of T7 phage DNApolymerase that lacks 3′-5′ exonuclease activity, or a mixture thereof.The DNA-dependent DNA polymerase is preferably Klenow Exo⁻ fragment ofDNA Polymerase I.

In another aspect to the invention, there is a method of differentiallyobtaining RNA from a sample comprising DNA and RNA, comprising providingthe mixture of DNA and RNA; heating said mixture to a temperature notexceeding about 75° C., to prevent denaturing of dsDNA; and subjectingthe mixture to a polymerase that replicates only single stranded RNAtemplates. The method may further comprise subjecting the mixture to aplurality of primers to form a ssRNA/dsDNA/primer mixture, wherein theprimers comprise nucleic acid sequence that is substantiallynon-self-complementary and substantially non-complementary to otherprimers in the plurality and wherein the primers comprise a knownnucleic acid sequence; and subjecting said ssRNA/dsDNA/primer mixture toa polymerase that primes and replicates only single stranded RNA, suchas M-MuLV reverse transcriptase, under conditions wherein the subjectingsteps generate a plurality of DNA molecules comprising the known nucleicacid sequence at each end.

In specific embodiments, the method further comprises the step ofamplifying a plurality of the DNA molecules through polymerase chainreaction, said reaction utilizing a primer complementary to the knownnucleic acid sequence.

In some embodiments of the present invention, there is a plurality of dsDNA molecules comprising genomic DNA, wherein when the molecules aredenatured to produce first and second strand molecules, each of whichcomprises a first and second end region at the respective ends of thefirst and second strand molecules, each of the first and second endregions of the first molecule comprise nucleic acid sequence that issubstantially non-self-complementary to sequence in the first and secondend regions in said first molecule, and each of the first and second endregions of the second molecule comprise nucleic acid sequence that issubstantially non-self-complementary to sequence in the first and secondend regions in said second molecule. In some embodiments, each of thefirst and second end regions of the first strand molecule aresubstantially non-complementary to the first and second end regions ofthe first strand of other molecules in the plurality, and wherein eachof the first and second end regions of the second strand molecule aresubstantially non-complementary to the first and second end regions ofthe second strand of other molecules in the plurality. The DNA moleculesmay further comprise a homopolymeric tag at the first and second endregions, wherein said end regions are penultimate on the molecules tothe homopolymeric tag. In specific embodiments, the amplified moleculesare further defined as a genomic library.

In additional embodiments of the present invention, there is a method ofsequencing a genome from a limited source of material, comprising thesteps of: obtaining at least one double stranded or single stranded DNAmolecule from a limited source of material; subjecting said doublestranded DNA molecule to heat to produce at least one single strandedDNA molecule; subjecting said single stranded DNA molecule to aplurality of primers to form a DNA molecule/primer mixture, wherein theprimers comprise nucleic acid sequence that is substantiallynon-self-complementary and substantially non-complementary to otherprimers in the plurality, wherein said sequence comprises in a 5′ to 3′orientation a constant region and a variable region; subjecting said DNAmolecule/primer mixture to a polymerase, under conditions wherein saidsubjecting steps generate a plurality of DNA molecules comprising theconstant region at each end; and amplifying a plurality of the DNAmolecules through polymerase chain reaction, said reaction utilizing aprimer complementary to the constant region; providing from theplurality of the amplified molecules a first and second sample ofamplified DNA molecules; sequencing at least some of the amplified DNAmolecules from the first sample to obtain at least one specific DNAsequence; incorporating homopolymeric poly C/poly G sequence to the endsof the amplified DNA molecules from the second sample to producehomopolymeric amplified molecules; amplifying at least some of thehomopolymeric amplified molecules from the second sample with a poly Cprimer and a primer complementary to the specific DNA sequence; andrepeating the sequencing and amplifying steps related to additionalspecific sequences, thereby producing a substantially complete contig ofthe genome.

In some embodiments, the incorporating of the homopolymeric sequencecomprises one of the following steps: extending the 3′ end of theamplified DNA fragments by terminal deoxynucleotidyl transferase in thepresence of dGTP; ligating an adaptor comprising the homopolymeric polyC/poly G sequence to the ends of the amplified DNA fragments; orreplicating the amplified DNA fragments with a primer comprising thehomopolymeric poly C sequence at its 5′ end and constant region at the3′ end. The sequencing step may be further defined as cloning theamplified DNA fragments from the first sample into a vector; andsequencing at least some of the cloned fragments.

The specific sequence of the amplified molecule may be obtained by thesequencing step of the first sample and wherein one or more of theadditional specific sequences is obtained by the sequencing step ofamplified molecules from the second sample. The limited source ofmaterial may be a microorganism substantially resistant to culturing, oran extinct species, for example. In specific embodiments, sequencing agenome is achieved with minimal redundancy.

In particular embodiments, the present invention is directed toamplification of DNA including whole-genome DNA from lower amounts ofsample than are generally sufficient to produce results from othermethods. The present disclosure provides methods and compositions tosuccessfully amplify DNA, including whole genomic DNA, from singlecells. Reproducible and accurate whole genome amplifications of DNA fromsingle cells are disclosed. Degenerate self-inert oligonucleotideprimers having a universal region and appropriate polymerase enzymes areused to amplify a substantial portion of genomic DNA from samplescontaining very low number of cells including single cells. Due to thereduced background amplification, clinical diagnosis from single cellDNA is improved.

The present disclosure relates to methods and compositions for theamplification of a whole genome, or whole transcriptome. In specificembodiments, a whole genome is amplified from a single cell. In aspecific embodiment the whole transcriptome is amplified from polyA+RNA, or in another embodiment, the whole transcriptome is amplifiedfrom total RNA.

In a particular aspect of the present invention, the invention isdirected to methods for the amplification of substantially the entiregenome or entire transcriptome without loss of representation ofspecific sites (herein defined as “whole genome amplification” and“whole transcriptome amplification”, respectively). In a specificembodiment, whole genome amplification includes simultaneousamplification of substantially all fragments of a genomic library. In afurther specific embodiment, “substantially entire” or “substantiallyall” refers to about 80%, about 85%, about 90%, about 95%, about 97%, orabout 99% of all sequences in a genome.

A skilled artisan recognizes that amplification of the whole genomewill, in some embodiments, include non-equivalent amplification ofparticular sequences over others, although the relative difference insuch amplification is not considerable. In an embodiment, the methodsand composition disclosed herein reproducibly amplify total DNA fromsingle cells about 1 million-fold to produce about 4-5 micrograms ofamplified DNA in about 2 hours. In some embodiments, the methods andcomposition disclosed herein are capable of producing greater than 90%amplification success rate with flow-sorted cells, faithfulrepresentation of GC-rich genomic regions, and about 94% correlationcoefficient for quantitative PCR (qPCR) data from replicate single-cellreactions.

The methods and compositions disclosed herein enhance single-copysensitivity and high specificity and also produce amplified DNAfragments that are suitable for copy number variation (CNV), SNPgenotyping, mutation detection, and sequencing. The methods andcompositions disclosed herein are capable of improved analytical andclinical performance for clinical testing of embryo biopsies and polarbody and other small samples such as characterize forensic andpaleobiology analyses. The methods and compositions disclosed herein arecapable of amplifying about 70-80% or 80-90% or 90-95% of the genome,e.g, human genome. The amplified products display high sequence fidelityand substantially lower background noise, e.g., less than 1% or 2% or 5%of the total amplified products. The methods and compositions disclosedherein provide enhanced performance with single cells that is equivalentto those obtained with more than 1,000 cells. In some embodiments, about70% of the probe sequences are highly represented among the amplicons.Reproducibility analysis by qPCR demonstrated that 60% of the locitested have a standard deviation less than 1 PCR cycle.

In certain embodiments of the invention, there is a method of amplifyinga substantial portion of genomic DNA from a single cell or a smallnumber of cells, the method comprising: (a) providing a samplecomprising a single cell or a small number of cells or DNA from thecells thereof; (b) providing degenerate self-inert oligonucleotideprimers selected from the group consisting of oligonucleotides listed inTable III and Table VII provided herein, wherein the primers comprise auniversal portion; (c) providing a suitable thermostable DNA polymeraseenzyme; and (d) providing conditions for amplifying the genomic DNA. Inspecific embodiments, the polymerase is a KAPA polymerase (KAPABiosystems). In certain aspects, the oligonucleotide primers comprise adetectable moiety. In specific cases, a small number of cells includesabout 1-5 cells. Exemplary thermostable polymerases include but are notlimited to KAPA 2G Robust (KAPA Biosystems); Taq Polymerase(BD/Clontech, Life Technologies); Phire (Finnzymes/New England Biolabs(NEB)); Pfu (Agilent Technologies/Stratagene); AccuPrime Pfx (LifeTechnologies); Phusion (Finnzymes/NEB); Vent (NEB); Deep Vent (NEB); andDyNAzyme (Finnzymes/NEB).

In specific embodiments of the invention, the nucleic acidmolecule/primer mixture is subjected to polymerase chain reaction havingpolymerization steps comprising two or more DNA denaturation steps.

In certain aspects of the invention, the method comprises (1) a firstseries of polymerase chain reaction steps comprising subjecting thenucleic acid molecule/primer mixture to a thermostable polymerase in thepresence of the primers under conditions having two or more cycling DNAdenaturation steps; and (2) a second series of polymerase chain reactionsteps using primers that comprise the constant region sequence.

Other objects, features and advantages of the present invention willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating the preferred embodiments of the invention,are given by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentinvention. The invention may be better understood by reference to one ormore of these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIG. 1 illustrates a schematic presentation of whole genome and wholetranscriptome amplification by incorporating known sequence withself-inert degenerate primers followed by PCR amplification. Dashedlines represent newly synthesized strands. Thicker lines represent theknown sequence.

FIG. 2 is a schematic presentation of design of exemplary self-inertdegenerate primers designed to eliminate their ability to formprimer-dimers.

FIG. 3A-3C provide an analysis of self-priming and extension ofdegenerate YN-primers (primers containing from 0 to about 6 completelyrandom bases (N) at the 3′ end, 10 degenerate pyrimidine bases Y, andthe known pyrimidine sequence YU at the 5′ end (FIG. 2)). In FIG. 3A, YNprimers containing 0, 1, 2 or 3 random N bases were used with or withoutdNTPs. In FIG. 3B, YN primers containing 0, 1, 2 or 3 random N bases anda model template oligonucleotide (Table III, primer 9) were used. InFIG. 3C, self-priming of YN-primers were tested. Note: Pyrimidine basesdo not stain efficiently with Sybr Gold. The presence of purine baseswithin the completely random portion (N) of YN-primers greatly increasesthe efficiency of staining these oligonucleotides.

FIG. 4 shows an assay for primer-dimer formation by degenerate YNprimers having from 0 to 6 completely random bases at the 3′ end or by aprimer comprised of T7 promoter sequence at the 5′ region and 6completely random bases at the 3′ end (Table III, primer 17) in humanwhole genome amplification with the Klenow Exo− fragment of DNAPolymerase I. The number of completely random bases (N) is shown at theend of each primer's abbreviation.

FIG. 5 demonstrates real-time PCR amplification of 5 ng aliquots ofwhole genome libraries synthesized with Klenow exo− fragment of DNAPolymerase I and self-inert degenerate primers described in FIG. 4.

FIG. 6A-6B show representation analysis of 30 exemplary human STSmarkers following whole genome amplification with exemplary degeneratepyrimidine YN primers specified in the description of FIG. 4 and theKlenow Exo− fragment of DNA Polymerase I. Aliquots corresponding to 10ng of amplified DNA were used for PCR analysis of STS markers. In FIG.6A, pyrimidine primers with 0 to 3 random 3′ bases were used for thelibrary synthesis step and in FIG. 6B, pyrimidine primers with 4 to 6random 3′ bases were used. The number of completely random bases (N) isshown at the end of each primer's abbreviation.

FIG. 7 shows real-time PCR amplification of 5 ng aliquots of wholegenome pre-amplified samples of thermally fragmented human genomic DNAwith Klenow Exo− fragment of DNA Polymerase I or Sequenase version 2using self-inert degenerate pyrimidine primer Y(N)₂ with 2 random basesat the 3′ end.

FIG. 8 demonstrates gel analysis of amplification products of thermallyfragmented human genomic DNA with Klenow Exo− fragment of DNA PolymeraseI or Sequenase version 2 using self-inert degenerate pyrimidine primerY(N)₂ as specified in the description to FIG. 7.

FIG. 9 shows representation analysis of 33 exemplary human STS markersfollowing whole genome amplification with exemplary self-inertdegenerate pyrimidine primer Y(N)₂ and Klenow Exo− fragment of DNAPolymerase I or Sequenase version 2. Aliquots corresponding to 10 ng ofamplified DNA were used for PCR analysis of STS markers.

FIG. 10 illustrates comparison between four self-inert degenerateprimers comprising four possible base pair combinations known not toparticipate in Watson-Crick base pairing and containing two completelyrandom bases at their 3′ ends in library synthesis reactions withSequenase version 2 DNA polymerase. Shown is quantitative real-time PCRamplification of aliquots corresponding to 5 ng of input DNA of thelibrary synthesis reactions. Abbreviations show the base composition ofthe self-inert degenerate primers.

FIG. 11A-11E show representation analysis of 35 exemplary human STSmarkers following whole genome amplification with self-inert degenerateprimers specified in the description to FIG. 10 and Sequenase version 2DNA polymerase or a combined sample in which equal amounts of fourindividual reactions each with a separate degenerate primer werecombined prior to PCR amplification of the STS markers. Aliquotscorresponding to 10 ng of amplified DNA were used for PCR analysis ofSTS markers. Abbreviations show the base composition of the self-inertdegenerate primers.

FIG. 12 demonstrates comparison between isothermal incubation at 24° C.for 60 min, a three-step incubation at 16° C., 24° C., and 37° C. for 20min each, and a cycling incubation for 19 cycles at 16° C., 24° C., and37° C. for 1 min each in whole genome amplification of human DNA withSequenase version 2 DNA polymerase and self-inert degenerate primerY(N)₂. Aliquots corresponding to 5 ng of input DNA of the WGA librarysynthesis reactions were amplified by quantitative real-time PCR.

FIG. 13 shows representation analysis of 17 Human STS markers followingwhole genome amplification with self-inert degenerate primer Y(N)₂ andSequenase version 2 DNA polymerase as detailed in the description toFIG. 12 Aliquots corresponding to 10 ng of amplified DNA were used forPCR analysis of STS markers.

FIG. 14 shows titration from 0.5 μM to 33 μM of self-inert degenerateprimer K(N)₂ in human WGA with Sequenase version 2 DNA polymerase.Aliquots corresponding to 5 ng of input DNA of the WGA library synthesisreactions were amplified by quantitative real-time PCR.

FIG. 15 shows representation analysis of 17 exemplary human STS markersfollowing whole genome amplification with exemplary self-inertdegenerate primer K(N)₂ applied at concentrations of 0.5 to 10 μM andSequenase version 2 DNA polymerase as specified in the description toFIG. 14. Aliquots corresponding to 10 ng of amplified DNA were used forPCR analysis of STS markers. Shown is a distribution plot of DNA amountsderived from quantitative real-time PCR. Horizontal bars representmedian values.

FIG. 16 shows titration from 5 ng to 100 ng of thermally fragmentedgenomic DNA in WGA reaction with self-inert degenerate primer K(N)₂ andSequenase version 2 DNA polymerase. Aliquots corresponding to 5 ng ofinput DNA of the WGA library synthesis reactions were amplified byquantitative real-time PCR.

FIG. 17 shows representation analysis of 20 exemplary human STS markersfollowing whole genome amplification of between 5 ng and 100 ng ofthermally fragmented DNA with self-inert degenerate primer K(N)₂ andSequenase version 2 DNA polymerase as specified in the description toFIG. 16. Aliquots corresponding to 10 ng of amplified DNA were used forPCR analysis of STS markers. Shown is a distribution plot of DNA amountsderived from quantitative real-time PCR. Horizontal bars representmedian values.

FIG. 18A-18C show the structure of the known primer with the ID tags.FIG. 18A illustrates replicable known primer with the known primersequence U at the 3′-end and individual ID sequence tag T at the 5′ end.FIG. 18B shows non-replicable known primer with the known primersequence U at the 3′ end, individual ID sequence tag T at the 5′ end,and non-replicable organic linker L between them. FIG. 18C shows 5′overhanging structure of the ends of DNA fragments in the WGA libraryafter amplification with non-replicable known primer.

FIG. 19 shows the process of synthesis of WGA libraries with thereplicable identification (ID) tag and their usage, for example forsecurity and/or confidentiality purposes, by mixing several librariesand recovering individual library by ID-specific PCR.

FIG. 20 shows the process of synthesis of WGA libraries with thenon-replicable ID tag and their usage, for example for security and/orconfidentiality purposes, by mixing several libraries and recoveringindividual libraries by ID-specific hybridization capture.

FIG. 21A-21C show the process of conversion of amplified WGA librariesinto libraries with additional G_(n) or C₁₀ sequence tag located at the3′ or 5′ end, respectively, of the universal known primer sequence Uwith subsequent use of these modified WGA libraries for targetedamplification of one or several specific genomic sites using universalprimer C₁₀ and unique primer P. FIG. 21A—library tagging byincorporation of a (dG)n tail using TdT enzyme; FIG. 21B—library taggingby ligation of an adaptor with the C₁₀ sequence at the 5′ end of thelong oligonucleotide; FIG. 21C—library tagging by secondary replicationof the WGA library using known primer with the C₁₀ sequence at the 5′end.

FIG. 22 shows the process for covalent immobilization of WGA library ona solid support.

FIG. 23A-23B show WGA libraries in the micro-array format. FIG. 23Aillustrates an embodiment utilizing covalent attachment of the librariesto a solid support. FIG. 23B illustrates an embodiment utilizingnon-covalent attachment of the libraries to a solid support.

FIG. 24 shows an embodiment wherein the immobilized WGA library may beused repeatedly.

FIG. 25 describes the method of WGA product purification utilizing anon-replicable known primer and magnetic bead affinity capture.

FIG. 26A-26B shows comparison between the whole genome amplificationdescribed in the present invention and a commercially available kit forDOP-PCR amplification. Aliquots of 5 ng and 20 pg of genomic DNA wereamplified with Klenow Exo− fragment of DNA polymerase I and 1 μM ofself-inert degenerate primer K(N)₂ or with DOP PCR Master™ Kit (RocheMolecular Biochemicals). (FIG. 26A) Real-time PCR amplification curvesfor libraries form 5 ng gDNA, 20 pg gDNA, or blank control. (FIG. 26B)Logarithmic distribution plots of 16 genomic STS markers amplified fromthe whole genome libraries amplified in FIG. 26A. Amplification withKlenow Exo− fragment of DNA polymerase I and self-inert degenerateprimer K(N)₂ was superior both in sensitivity and in representation ofgenomic markers as compared to that with DOP PCR

FIG. 27 displays the amplification curves of libraries generated fromDNA isolated from serum collected in a serum separator tube. Theamplification was performed for 17 cycles.

FIG. 28A-28B represent the analysis of the amplified products from serumDNA. In FIG. 28A, there is gel analysis of both serum DNA (Right) andamplified products (Left). Both the starting serum DNA and amplifiedmaterial demonstrate a size range of 200 bp to 1.6 kb, indicating thatthe amplified material maintains the same size distribution as the DNAisolated from the serum. In FIG. 28B, there is real-time STS analysis of8 STS sites in amplified products from serum DNA. The solid linecrossing the entire graph represents both the amount of DNA added to theSTS assay based on optical density, and the average value of the 8 STSsites. The short line represents the median value of the 8 STS sitesobtained by real-time PCR analysis. All 8 sites were represented withina factor of 5 of the mean amplification.

FIG. 29 illustrates amplification of single blood nucleated cells by amethod of the present invention.

FIG. 30 shows amplification of single sperm cells by a method of thepresent invention.

FIG. 31 shows dilution of hair follicle samples for an exemplaryforensic application of a method described herein.

FIG. 32 illustrates amplification of a single copy chromosome.

FIG. 33 shows micro-array hybridization analysis of the amplified DNAfrom a single-cell DNA produced by whole genome amplification.

FIG. 34 illustrates single-cell DNA arrays for detection and analysis ofcells, such as cancer cells.

FIG. 35, panels A-D show real-time PCR amplification using twoX-chromosome specific primer pairs to evaluate loci copy number valuesin WGA libraries synthesized from patient DNA of known aneuploidies ofXO, XX, and XXX. Panels A and C show curves from each of 5 individualamplifications. Panels B and D show mixtures of the five librariestested in triplicate demonstrating the maintenance of copy numberinformation in WGA libraries.

FIG. 36 shows real-time PCR amplification of WTA libraries prepared from10 ng and 100 ng from human B-lymphocyte RNA using self-inert degenerateprimer K(N)2 and MMLV reverse transcriptase. Amplification profiles showabout a one-cycle difference between 100 ng of input and 10 ng of inputtemplate.

FIG. 37 shows real-time PCR amplification of WTA libraries prepared withtwo different self-inert primers K(N)₂ and K(T20) and their combination.Significant improvement was observed when a combination of K(N)₂ andK(T20) is used.

FIG. 38 shows gel electrophoretic analysis of amplified WTA libraries.The observed pattern of ethidium bromide staining visualized byfluorescence transilumination (Fluor-S, Bio-Rad) shows the range offragment sizes and intensity resulting from varying the amounts of inputRNA in library synthesis and from varying the primer combinationsutilized. 100 ng of input RNA yields larger products without significanteffect of the primer K(T20). Libraries from 10 ng of input RNA yieldgenerally smaller amplification products and show significantimprovement with the addition of K(T20) primer.

FIG. 39 provides quantitative real-time PCR analysis of amplified WTAlibraries. The plots show analysis of 11 sites corresponding to humanSTS markers. The long bar in each column represents the average valuewhile the short bar represents the median value. The line at 10 ngrepresents the amount of amplified DNA, by spectrophotometric analysis,added to each assay. All 11 sites were detected in each sample,indicating that all sites were efficiently amplified in all samples. Therepresentation of these 11 markers is similar between the K(N2) andK(N2)+K(T20) 100 ng libraries. The distribution is wider for the 10 nglibraries than the 100 ng libraries and the distribution of the 10 ngK(N2) library is slightly broader than the 10 ng K(N2)+K(T20) library.

FIG. 40A-40C illustrate results of real-time PCR analysis of threeexemplary expressed mRNA loci at three different distances from the 3′end using human STS markers. The lengths of the mRNA for each STS are6,642 bp for STS 42, 3,100 bp for STS 85, and 9,301 bp for STS 119. Thedistances from the 3′ end for the STS 42 locus are 1,087 bp, 1,795 bp,and 5,835 bp. The distances from the 3′ end for the STS 85 locus are 77bp, 1,331 bp, and 1,827 bp. The distances from the 3′ end for the STS119 locus are 1,834 bp, 3,746 bp, and 5,805 bp. Results are shown for100 ng and 10 ng input libraries with either K(N)₂ or K(N)₂+K(T20)library synthesis primers. Representation of marker sequences for WTAlibraries at different lengths along a specific transcript showconsistent results between libraries made from different quantities ofRNA and display only minor improvements in 3′ representation with theaddition of K(T20).

FIG. 41 illustrates results of real-time PCR analysis of input templateand two principal MgCl₂ concentrations typically used with the RNAdependent DNA polymerase, reverse transcriptase.

FIG. 42 shows the resulting representation of specific sites analyzed byreal-time PCR for their relative abundance within a subset of thesamples described in FIG. 41 (10 ng and 0.25 ng input template; 3 mM and10 mM MgCl₂ concentration). As is typical of such experiments, samplesthat amplify more robustly also show better representation of specificsites.

FIG. 43 illustrates the effect of MgCl₂ concentration on WTAamplification of total RNA. Using a constant 10 ng template RNA theMgCl₂ concentration was varied over a range of between 3 mM and 12 mM. Aclear dependence is observed in WTA performance under these reactionconditions, with optimal amplification performance occurring between 6mM and 10 mM.

FIG. 44A-44B demonstrates the selective amplification of single strandedtemplates in WTA library synthesis using either DNA or RNA with orwithout denaturation. FIG. 44A shows real-time PCR curves of theamplification of these libraries. FIG. 44B shows the resulting productsrun on a 0.8% agarose gel stained with ethidium bromide. Only about 1%of DNA sample can be converted into library amplimers withoutdenaturation, while denaturation had little effect on RNA templates.

FIG. 45 illustrates principle of selective amplification of DNA and RNAfrom a total nucleic acid isolate using self-inert degenerate primers incombination with Klenow Exo-fragment of DNA polymerase I andheat-denatured nucleic acid (WGA) or MMLV reverse transcriptase andnon-denatured nucleic acid (WTA), and a hypothetical device forisolation of DNA and RNA by selective amplification from total nucleicacid preparation.

FIG. 46A-46B show the inhibitory effect of poly-C tags on amplificationof synthesized WGA libraries. FIG. 46A shows real-time PCR amplificationchromatograms of different length poly-C tags incorporated bypolymerization. FIG. 46B shows delayed kinetics or suppression ofamplification of C-tagged libraries amplified with corresponding poly-Cprimers.

FIG. 47A-47B display real-time PCR results of targeted amplificationusing a specific primer and the universal C₁₀ tag primer. FIG. 47A showsthe sequential shift with primary and secondary specific primers with acombined enrichment above input template concentrations. FIG. 47B showsthe effect of specific primer concentration on selective amplification.Real-time PCR curves show a gradient of specific enrichment with respectto primer concentration.

FIG. 48A-48B detail the individual specific site enrichment for eachunique primary oligonucleotide in the multiplexed targetedamplification. FIG. 48A shows values of enrichment for each siterelative to an equal amount of starting template, while FIG. 48Bdisplays the same data as a histogram of frequency of amplification.

FIG. 49A-49B. FIG. 49A shows the analysis of secondary “nested”real-time PCR results for 45 multiplexed specific primers. Enrichment isexpressed as fold amplification above starting template ranging from100,000 fold to over 1,000,000 fold. FIG. 49B shows the distributionfrequency for all 45 multiplexed sites.

FIG. 50 shows a schematic representation of a whole genome sequencingproject using tagged libraries synthesized from limited startingmaterial. Libraries provide a means to recover precious or rare samplesin an amplifiable form that can function both as substrate for cloningapproaches and through conversion to C-tagged format a directedsequencing template for gap filling and primer walking.

FIG. 51 shows a diagram illustrating universality of the nucleic acidamplification methods of the present invention and their compatibilitywith different sources of DNA or RNA, and the diversity of possibleapplications for the amplified material.

FIG. 52 demonstrates an example of Background Subtracted RFUamplification curves for replicate single-cell and control no-cell wholegenome amplification (WGA) reactions monitored on a Bio-Rad I-Cycler iQ.

FIG. 53 shows PCR cycles for 5 cells, 1 cell and control (0 cells) asstarting materials.

FIG. 54A-54B show locus-specific PCR QC—testing of single-cell wholegenomic amplification of DNA; (FIG. 54A) Locus-specific PCR of genomicDNA with increasing number cell-equivalents; (FIG. 54B) Locus-specificPCR of whole genome-amplified DNA from 1, 10, 100, and 1000cell-equivalents (DNA amplified from a single cell gives the same testresult as from 1,000 cells).

FIG. 55 compares cell to cell variation for 2 cells in 24 Q PCR assays;single-cell whole genome amplification produces highly reproduciblerepresentation of multiple loci tested in different single cells.

FIG. 56 illustrates reproducibility of representation, assayed byindividual QPCR reactions across 10 replicate single cells.

FIG. 57A-57B illustrate a comparison between a particular exemplarymethod of the claimed invention (FIG. 57A) with a method known in theart (FIG. 57B).

DETAILED DESCRIPTION OF THE INVENTION

In keeping with long-standing patent law convention, the words “a” and“an” when used in the present specification in concert with the wordcomprising, including the claims, denote “one or more.”

The practice of the present invention will employ, unless otherwiseindicated, conventional techniques of molecular biology, microbiology,recombinant DNA, and so forth which are within the skill of the art.Such techniques are explained fully in the literature. See e.g.,Sambrook, Fritsch, and Maniatis, MOLECULAR CLONING: A LABORATORY MANUAL,Second Edition (1989), OLIGONUCLEOTIDE SYNTHESIS (M. J. Gait Ed., 1984),ANIMAL CELL CULTURE (R. I. Freshney, Ed., 1987), the series METHODS INENZYMOLOGY (Academic Press, Inc.); GENE TRANSFER VECTORS FOR MAMMALIANCELLS (J. M. Miller and M. P. Calos eds. 1987), HANDBOOK OF EXPERIMENTALIMMUNOLOGY, (D. M. Weir and C. C. Blackwell, Eds.), CURRENT PROTOCOLS INMOLECULAR BIOLOGY (F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore,J. G. Siedman, J. A. Smith, and K. Struhl, eds., 1987), CURRENTPROTOCOLS IN IMMUNOLOGY (J. E. coligan, A. M. Kruisbeek, D. H.Margulies, E. M. Shevach and W. Strober, eds., 1991); ANNUAL REVIEW OFIMMUNOLOGY; as well as monographs in journals such as ADVANCES INIMMUNOLOGY. All patents, patent applications, and publications mentionedherein, both supra and infra, are hereby incorporated herein byreference.

U.S. Provisional Patent Application No. 60/453,071, filed Mar. 7, 2003is hereby incorporated by reference herein in its entirety. U.S.Nonprovisional patent application Ser. No. 10/797,333 is also herebyincorporated by reference herein in its entirety. U.S. PatentApplication 20030143599 is also incorporated by reference herein in itsentirety.

I. Definitions

The term “base analog” as used herein refers to a compound similar toone of the four DNA bases (adenine, cytosine, guanine, and thymine) buthaving a different composition and, as a result, different pairingproperties. For example, 5-bromouracil is an analog of thymine butsometimes pairs with guanine, and 2-aminopurine is an analog of adeninebut sometimes pairs with cytosine.

The term “backbone analog” as used herein refers to a compound whereinthe deoxyribose phosphate backbone of DNA has been modified. Themodifications can be made in a number of ways to change nucleasestability or cell membrane permeability of the modified DNA. Forexample, peptide nucleic acid (PNA) is a new DNA derivative with anamide backbone instead of a deoxyribose phosphate backbone. Otherexamples in the art include methylphosphonates.

The term “blocked 3′ end” as used herein is defined as a 3′ end of DNAlacking a hydroxyl group.

The term “blunt end” as used herein refers to the end of a doublestranded DNA molecule having 5′ and 3′ ends, wherein the 5′ and 3′ endsterminate at the same position. Thus, the blunt end comprises no 5′ or3′ overhang.

The term “complementarity” as used herein refers to the ability to forma Watson-Crick base pair through specific hydrogen bonds.

The term “contig” as used herein refers to a contiguous (continuous)sequence of DNA constructed from overlapping sequences.

The term “degenerate” as used herein refers to a nucleotide or series ofnucleotides wherein the identity can be selected from a variety ofchoices of nucleotides, as opposed to a defined sequence. In specificembodiments, there can be a choice from two or more differentnucleotides. In further specific embodiments, the selection of anucleotide at one particular position comprises selection from onlypurines, only pyrimidines, or from non-pairing purines and pyrimidines.

The term “self-inert” as used herein refers to the inability of a primeror a mixture of primers to self-prime and initiate DNA synthesis in thepresence of DNA polymerase and dNTPs but in the absence of other DNAtemplates. It may also refer to a collective set of mRNAs in a cell.

The term “DNA immortalization” as used herein refers to the conversionof a mixture of DNA molecules into a form that allows repetitive,unlimited amplification without loss of representation and/or withoutsize reduction. In a specific embodiment, the mixture of DNA moleculescomprises more than one copy of a particular DNA sequence. In anotherspecific embodiment, the mixture of DNA molecules comprises a genome.

The term “genome” as used herein is defined as the collective gene setcarried by an individual, cell, or organelle.

The term “genomic DNA” as used herein is defined as DNA materialcomprising the partial or full collective gene set carried by anindividual, cell, or organelle.

The term “transcriptome” as used herein is defined as the collective RNAset expressed within a cell.

The term “hybridization” as used herein refers to a process of formationof double stranded DNA regions between one, two or many complementarysingle stranded DNA molecules. In some embodiments, however, triplestranded DNA regions are generated through hybridization.

The term “minimal redundancy” as used herein refers to a minimal numberof sequenced DNA fragments that produces a contig. A skilled artisanrecognizes this is as opposed to “shotgun” sequencing where highredundancy is necessary to complete all gaps. Typically, the redundancyof “shotgun” sequencing is about 10-15 (where redundancy=total amount ofsequenced DNA divided by the size of the genome), whereas with minimalredundancy the redundancy may be between 1 and about 2.

The term “non-canonical or non-Watson-Crick base pair” as used hereinrefers to all possible interactions between bases that do not includestandard (Watson-Crick) A-T and G-C pairing. In a specific embodiment,the non-canonical base pair comprises an adenine nucleobase and aguanine nucleobase, an adenine nucleobase and a cytosine nucleobase, acytosine nucleobase and a thymidine nucleobase, a guanine nucleobase anda thymidine nucleobase, an adenine nucleobase and an adenine nucleobase,a guanine nucleobase and a guanine nucleobase, a cytosine nucleobase anda cytosine nucleobase, or a thymidine nucleobase and a thymidinenucleobase.

The term “non-complementary” refers to nucleic acid sequence that lacksthe ability to form intermolecularly at least one Watson-Crick base pairthrough specific hydrogen bonds.

The term “non-self-complementary” refers to nucleic acid sequence thatlacks the ability to form intramolecularly at least one Watson-Crickbase pair through specific hydrogen bonds.

The term “non strand-displacing polymerase” as used herein is defined asa polymerase that extends until it is stopped by the presence of, forexample, a downstream primer. In a specific embodiment, the polymeraselacks 5′-3′exonuclease activity.

The term “randomly fragmenting” as used herein refers to fragmenting aDNA molecule in a non-ordered fashion, such as irrespective of thesequence identity or position of the nucleotide comprising and/orsurrounding the break. In a specific embodiment, the randomfragmentation is mechanical, chemical, or enzymatic, by well-knownmethods in the art.

The term “RNA immortalization” as used herein refers to the conversionof a mixture of RNA molecules, such as a transcriptome, into a form thatallows repetitive, unlimited amplification without loss ofrepresentation and/or without size reduction. In a specific embodiment,a transcriptome is defined as a collection of transcribed mRNA moleculesfrom a cell, an individual, or an organelle.

The term “single stranded nucleic acid molecule/primer mixture” as usedherein refers to a mixture comprising at least one single strandednucleic acid molecule wherein at least one primer, as described herein,is hybridized to a region in said single stranded nucleic acid molecule.In specific embodiments, multiple degenerate primers comprisecomplementary sequence to at least some part of the single strandednucleic acid molecule. In further specific embodiments, the mixturecomprises a plurality of single stranded nucleic acid molecules havingmultiple degenerate primers hybridized thereto. In additional specificembodiments, the single stranded nucleic acid molecule is DNA or RNA.

The term “strand-displacing polymerase” as used herein is defined as apolymerase that will displace downstream fragments as it extends. In aspecific embodiment, the polymerase comprises 5′-3′ exonucleaseactivity.

The term “substantially incapable” as used herein refers to a majorityof polynucleotides being incapable of an activity upon subjection tostandard conditions known in the art. In a specific embodiment, theactivities include self-hybridization; self-priming; hybridization toanother polynucleotide in the plurality; initiation of a polymerizationreaction in the plurality, or a combination thereof. In a specificembodiment, the term refers to at least about 70% of a primer moleculebeing comprised of two noncomplementary and non-self-complementarynucleotides, more preferably at least about 75%, more preferably atleast about 80%, more preferably at least about 85%, more preferably atleast about 90%, more preferably at least about 95%, more preferably atleast about 97%, more preferably at least about 99%, and most preferably100% of a primer molecule being comprised of two noncomplementary andnon-self-complementary nucleotides.

The term “substantially non-self-complementary and substantiallynon-complementary” as used herein refers to a plurality of primers thatlack the ability to form intramolecularly and intermolecularly aWatson-Crick base pair through specific hydrogen bonds. In a specificembodiment, at least about 70% of a primer molecule in the plurality iscomprised of two noncomplementary and non-self-complementarynucleotides, more preferably at least about 75%, more preferably atleast about 80%, more preferably at least about 85%, more preferably atleast about 90%, more preferably at least about 95%, more preferably atleast about 97%, more preferably at least about 99%, and most preferably100% of a primer molecule in the plurality is comprised of twononcomplementary and non-self-complementary nucleotides.

The term “thermophilic DNA polymerase, as used herein refers to aheat-stable DNA polymerase.

A skilled artisan recognizes that there is a conventional single lettercode in the art to represent a selection of nucleotides for a particularnucleotide site. For example, R refers to A or G; Y refers to C or T; Mrefers to A or C; K refers to G or T; S refers to C or G; W refers to Aor T; H refers to A or C or T; B refers to C or G or T; V refers to A orC or G; D refers to A or G or T; and N refers to A or C or G or T. Thus,a YN primer comprises at least one, and preferably more, series ofdinucleotide sets each comprising a C or a T at the first position andan A, C, G, or T at the second position. These dinucleotide sets may berepeated in the primer (and/or adaptor).

II. Preparation of DNA Libraries for Whole Genome and WholeTranscriptome Amplification by Incorporating a Known Universal SequenceUsing Self-Inert Degenerate Primers

In embodiments of the present invention, there is whole genome or wholetranscriptome amplification comprising incorporation of known universalsequence followed by a subsequent PCR amplification step using a knownuniversal primer complementary to at least part of the known universalsequence. In a specific embodiment, the primers for incorporating theknown universal sequence comprise a degenerate region, and in furtherspecific embodiments, the known universal sequence and the degenerateregion comprise non-self-complementary nucleic acid sequence. Thus,there is significant reduction in self-hybridization and intermolecularprimer hybridization compared to primers lacking non-self-complementarysequence.

Formation of primer dimers is a common problem in existing methods forDNA or RNA amplification using random primers. In order to achieveefficient priming for each individual sequence, random primers must beapplied at very high concentrations. The efficiency of annealing to aspecific target DNA or RNA template or the entire population of templatemolecules is greatly reduced by the formation of primer-dimers resultingfrom the high primer concentrations required for efficient priming.

Other problems known in the art when using random primers to amplify DNAinclude an inability to amplify the genome in its entirety due to locusdropout (loss), generation of short amplification products, and in somecases, the inability to amplify degraded or artificially fragmented DNA.

The described invention utilizes a novel type of oligonucleotide primercomprising at least as the majority of its sequence only two types ofnucleotide bases that do not participate in stable Watson-Crick pairingwith each other, and thus do not self-prime. The primers comprise aconstant known sequence at their 5′end and a variable degeneratenucleotide sequence located 3′ to the constant known sequence. There arefour possible two-base combinations known not to participate inWatson-Crick base pairing: C-T, G-A, A-C and G-T. They suggest fourdifferent types of degenerate primers that should not form a singleWatson-Crick base pair that could lead to the generation ofprimer-dimers in the presence of DNA polymerase and dNTPs. These primersare illustrated in FIG. 2A and are referred to as primers Y, R, M and K,respectively, in accordance with common nomenclature for degeneratenucleotides: Y=C or T, R=G or A, M=A or C and K=G or T.

For example, Y-primers have a 5′ known sequence Y_(U) comprised of C andT bases and a degenerate region (Y)₁₀ at the 3′ end comprising ten, forexample, randomly selected pyrimidine bases of C and T. R-primers have a5′ known sequence R_(U) comprised of G and A bases and a degenerateregion (R)₁₀ at the 3′ end comprising ten, for example, randomlyselected purine bases of G and A. M-primers have a 5′ known sequenceM_(U) comprised of A and C bases and a degenerate region (M)₁₀ at the 3′end comprising ten for example, randomly selected bases of A and C.Finally, K-primers have a 5′ known sequence K_(U) comprised of G and Tbases and a degenerate region (K)₁₀ at the 3′ end comprising ten, forexample, randomly selected bases of G and T. Primers of the describeddesign will not self-prime and thus will not form primer dimers. Forthis reason, the term “self-inert primers” is used herein. However, theywill prime at target sites containing the corresponding Watson-Crickbase partners, albeit with reduced overall frequency compared tocompletely random primers. In specific embodiments, these primers underspecific conditions are capable of forming primer dimers, but at agreatly reduced level compared to primers lacking such structure.

In some embodiments, these primers are supplemented with a completelyrandom (i.e. containing any of the four bases) short nucleotide sequenceat their 3′ end. Such primers are shown on FIG. 2 and labeled as YN, RN,MN and KN. If a limited number of completely random bases are present atthe 3′ end of the Y, R, M or K primers, that will increase their primingfrequency, yet maintain limited ability for self-priming. By using adifferent number of completely random bases at the 3′ end of thedegenerate Y, R, M or K primers and by carefully optimizing the reactionconditions, one can precisely control the outcome of the polymerizationreaction in favor of the desired DNA product with minimum primer-dimerformation.

Thus, in the first step of library synthesis primers of the describeddesign are randomly incorporated in an extension/polymerization reactionwith a DNA polymerase possessing at least a limited strand-displacementactivity. The resulting branching process creates DNA molecules havingknown (universal) self-complementary sequences at their ends. In asecond step referred to as the “amplification” step, these molecules areamplified exponentially by polymerase chain reaction using Taqpolymerase (or other thermostable DNA polymerase) and a single primercorresponding to at least part of the known 5′-tail of the randomprimers. FIG. 1 presents a schematic outline of the invention. Theinvention overcomes major problems known in the art for DNA and RNAamplification by previously described random primers.

1. Source of Nucleic Acid

Single-stranded or double-stranded nucleic acid of any source orcomplexity, or fragments thereof, can be used as a source material andamplified by the method described in the invention. That is, in someembodiments single stranded DNA is obtained and processed according tothe methods described herein, and in other embodiments double strandedDNA is obtained and manipulated to generate ssDNA, wherein the ssDNA issubjected to the methods described herein. In a specific embodiment,dsDNA is denatured with heat, chemical treatment (such as alkaline pH),mechanical manipulation, radiation, or a combination thereof. In anotherspecific embodiment, substantially single stranded RNA is obtained andprocessed according to the methods described herein. In a specificembodiment, total nucleic acid is obtained as a mixture of doublestranded DNA and single stranded RNA molecules and then processed toselectively amplify the DNA fraction or RNA fraction only, or bothseparately, or both in a mixture.

2. Design of Degenerate Primers

FIG. 2 illustrates the design of degenerate primers utilized in thisaspect of the invention. In principle, the invention employs applicationof oligonucleotide primers comprising a constant known sequence at their5′end (which may be referred to as universal sequence) and a variabledegenerate nucleotide sequence at their 3′ end, each comprised of any ofat least four possible base combinations known not to participate inWatson-Crick base pairing. The possible primer compositions includepyrimidines only (C and T), purines only (A and G), or non-pairingpurines and pyrimidines (A and C or G and T). The last combination (Gand T) is known in the art to permit non-canonical Watson-Crickbase-pairing. In a preferred embodiment, the G and T pair is utilized inthe invention. In a specific embodiment, the primers comprise a constantpart of about 18 base sequence comprised of C and T, G and A, A and C,or G and T bases at the 5′ end, followed by about 10 random Y, R, M or Kbases, respectively, and between 0 and about 6 completely random bases,N, at the 3′ end (FIG. 2, Table III, primers 1-7). Examples 1 and 2 showthat Y and YN primers form only a limited amount of primer-dimers, andthis is proportional to the number of completely random bases N at their3′ termini. In contrast, a primer of similar design but comprised ofbases that can participate in Watson-Crick base-pairing generates anexcessive amount of primer-dimers, which greatly reduces the efficiencyof DNA or RNA amplification (see Example 2).

The choice of primers will depend on the base composition, complexity,and the presence and abundance of repetitive elements in the target DNAor RNA. By combining the products of individual amplification reactionswith degenerate primers comprising different non-Watson-Crick pairs, buthaving the same known sequence at the ends, one can achieve the highestpossible level of representative and uniform DNA amplification. Askilled artisan recognizes how to select the optimal primers andreaction conditions to achieve the desired result.

Example 2 describes a comparison of different pyrimidine-only primers intheir ability to form primer-dimers, efficiency of amplification, anduniformity (representation of randomly selected genomic markers) in ahuman whole genome amplification reaction with Klenow fragment of DNAPolymerase I. Of all pyrimidine-only primers tested, primers with tworandom 3′ bases (Y(N)₂) result in the most uniform whole genomeamplification and at the same time form undetectable amounts of primerdimers. Thus, in a preferred embodiment degenerate primers comprisingbetween about 1 and about 3 completely random bases at their 3′ end areutilized.

3. Choice of DNA Polymerases

In a preferred embodiment, a DNA polymerase is utilized that possessesstrand-displacement activity. Preferred strand-displacement DNApolymerases are: Klenow fragment of E. coli DNA polymerase I, exo− DNApolymerases of the T7 family, i.e. polymerases that require hostthioredoxin subunit as co-factor, such as: T7, T3, fI, fII, W31, H, Y,gh-1, SP6, or All22, Studier (1979), exo− Bst large fragment, Bca DNApolymerase, 9° Nm polymerase, MMLV Reverse Transcriptase, AMV ReverseTranscriptase, HIV Reverse Transcriptase, phage f29 polymerase, phage M2polymerase, phage fPRD1 polymerase, exo− VENT polymerase, and phage T5exo− DNA polymerase.

Klenow exo− fragment of DNA Polymerase I, phage T7 DNA polymerase withreduced or eliminated 3′-5′ exonuclease activities, and MMLV ReverseTranscriptase are most preferred in the present invention. Thus, in apreferred embodiment the Klenow exo− fragment of DNA Polymerase I, orSequenase version 2 is used as the polymerase for whole genomeamplification (Example 2), and MMLV reverse transcriptase is used as thepolymerase for whole transcriptome amplification (Example 14).

4. Reaction Conditions

In general, factors increasing priming efficiency, such as reducedtemperature or elevated salt and/or Mg²⁺ ion concentration, inhibit thestrand-displacement activity and the rate of DNA polymerases, andelevated temperatures and low Mg²⁺ ion or salt concentrations increasethe efficiency of polymerization/strand-displacement but reduce thepriming efficiency. On the other hand, factors promoting efficientpriming also increase the chances of primer-dimer formation.Strand-displacement activity can be facilitated by several proteinfactors. Any polymerase that can perform strand-displacementreplication, in the presence or in the absence of suchstrand-displacement or processivity enhancing factors, is suitable foruse in the disclosed invention, even if the polymerase does not performstrand-displacement replication in the absence of such factor. Factorsuseful in strand-displacement replication are (i) any of a number ofsingle-stranded DNA binding proteins (SSB proteins) of bacterial, viral,or eukaryotic origin, such as SSB protein of E. coli, phage T4 gene 32product, phage T7 gene 2.5 protein, phage Pf3 SSB, replication protein ARPA32 and RPA14 subunits (Wold, 1997); (ii) other DNA binding proteins,such as adenovirus DNA-binding protein, herpes simplex protein ICP8,BMRF1 polymerase accessory subunit, herpes virus UL29 SSB-like protein;(iii) any of a number of replication complex proteins known toparticipate in DNA replication such as phage T7 helicase/primase, phageT4 gene 41 helicase, E. coli Rep helicase, E. coli recBCD helicase, E.coli and eukaryotic topoisomerases (Champoux, 2001).

The exact parameters of the polymerization reaction will depend on thechoice of polymerase and degenerate primers and a skilled artisanrecognizes based on the teachings provided herein how to modify suchparameters. By varying the number of random bases at the 3′ end of thedegenerate primers and by carefully optimizing the reaction conditions,formation of primer-dimers can be kept to a minimum and at the same timethe amplification efficiency and representation can be maximized.

Random fragmentation of DNA, and if necessary, RNA can be performed bymechanical, chemical, or enzymatic treatment as described. In apreferred embodiment, DNA is fragmented by heating at about 95° C. inlow salt buffers such as TE (10 mM Tris-HCl, 1 mM EDTA, having pHbetween 7.5 and 8.5) or TE-L (10 mM Tris-HCl, 0.1 mM EDTA, having pHbetween 7.5 and 8.5) for between about 1 min and about 10 min (forexample, see U.S. patent application Ser. No. 10/293,048, filed Nov. 13,2002, incorporated by reference herein in its entirety).

An exemplary library synthesis reaction of the present invention isperformed in a mixture having volume ranging between about 10 and about25 μl. The reaction mixture preferably comprises about 0.5 to about 100ng of thermally or mechanically fragmented DNA, or in particularembodiments less than about 0.5 ng DNA, about 0.5-about 30 μM ofself-inert degenerate primer, about 0-about 200 nM of known sequenceprimer (i.e., primer corresponding to the known 5′ end of the respectivedegenerate primer), between about 2 and about 10 units of Klenow Exo⁻(New England Biolabs) or Sequenase version 2 (USB Corporation), between0-about 360 ng SSB protein, and between about 5-about 10 mM MgCl₂, andbetween 0 and about 100 mM NaCl. The reaction buffer preferably has abuffering capacity that is operative at physiological pH between about6.5 and about 9. Preferably, the incubation time of the reaction isbetween about 10-about 180 min, and the incubation temperature betweenabout 12° C. and about 37° C. Incubation is performed by cycling betweenabout 12° C. and about 37° C. for a total of 3 to 5 min per cycle, orpreferably by a single isothermal step between about 12° C. and about30° C. or sequential isothermal steps between about 12° C. and about 37°C. The reaction is terminated by addition of a sufficient amount of EDTAto chelate Mg²⁺ or preferably by heat-inactivation of the polymerase, orboth.

In a preferred embodiment of the present invention, the librarysynthesis reaction is performed in a volume of about 15 μl. The reactionmixture comprises about 5 ng or less of thermally or mechanicallyfragmented DNA, for example, about 2 μM of self-inert degenerate primerK(N)₂ comprising G and T bases at the known and degenerate regions and 2completely random 3′ bases, (Table III, primer #14), between about 2units and about 4 units of Sequenase version 2 DNA polymerase (USBCorporation), between about 5 mM and about 10 mM MgCl₂, about 100 mMNaCl, about 10 mM Tris-HCl buffer having pH of about 7.5, and about 7.5mM dithiothreitol. Preferably, the incubation time of the reaction isbetween about 60 min and about 120 min and the incubation temperature isabout 24° C. in an isothermal mode or in another preferred embodiment bysequential isothermal steps at between about 16° C. and about 37° C.

In another preferred embodiment of the present invention, the librarysynthesis reaction is performed in a volume of about 20 μl. The reactionmixture comprises about 25 ng or less of thermally or fragmented orunfragmented RNA, for example, about 1 μM of self-inert degenerateprimer K(N)₂ comprising G and T bases at the known and degenerateregions and 2 completely random 3′ bases, (Table III, primer #14), about200 nM of a primer K(T)₂₀ comprising G and T bases at the 5′ known andpoly T bases at the 3′ end (Table III, primer #19) between about 50units and about 200 units of MMLV Reverse transcriptase (EpicentreCorporation), between about 3 mM and about 10 mM MgCl₂, about 75 mM KCl,about 50 mM Tris-HCl buffer having pH of about 8.3, and about 10 mMdithiothreitol. Preferably, the incubation time of the reaction isbetween about 30 min and about 120 min and the incubation temperature isabout 42° C. in an isothermal mode or in another preferred embodiment bysequential isothermal steps at between about 24° C. and about 42° C.

A typical amplification step with known sequence primer comprisesbetween about 1 and about 10 ng of library synthesis products andbetween about 0.3 and about 2 μM of known sequence primer in a standardPCR reaction well known in the art, under conditions optimal forthermostable DNA polymerases, such as Taq DNA polymerase, Pfupolymerase, or derivatives and mixtures thereof. For sequences known tobe difficult to amplify, such as those high in G/C content that areknown otherwise to benefit from PCR optimization efforts such astemperature and time of denaturation and polymerization steps, reactionadditives such as DMSO and/or 7-Deaza dGTP may also improverepresentation in libraries constructed by the method of the invention.

III. Nucleic Acids

The term “nucleic acid” or “polynucleotide” will generally refer to atleast one molecule or strand of DNA, RNA, DNA-RNA chimera or aderivative or analog thereof, comprising at least one nucleobase, suchas, for example, a naturally occurring purine or pyrimidine base foundin DNA (e.g. adenine “A,” guanine “G,” thymine “T” and cytosine “C”) orRNA (e.g. A, G, uracil “U” and C). The term “nucleic acid” encompassesthe terms “oligonucleotide” and “polynucleotide.” The term“oligonucleotide” refers to at least one molecule of between about 3 andabout 100 nucleobases in length. The term “polynucleotide” refers to atleast one molecule of greater than about 100 nucleobases in length.These definitions generally refer to at least one single-strandedmolecule, but in specific embodiments will also encompass at least oneadditional strand that is partially, substantially, or fullycomplementary to at least one single-stranded molecule. Thus, a nucleicacid may encompass at least one double-stranded molecule or at least onetriple-stranded molecule that comprises one or more complementarystrand(s) or “complement(s)” of a particular sequence comprising astrand of the molecule. As used herein, a single stranded nucleic acidmay be denoted by the prefix “ss”, a double stranded nucleic acid by theprefix “ds”, and a triple stranded nucleic acid by the prefix “ts.”

Nucleic acid(s) that are “complementary” or “complement(s)” are thosethat are capable of base-pairing according to the standard Watson-Crick,Hoogsteen or reverse Hoogsteen binding complementarity rules. However,in a specific embodiment, a primer of the present invention comprises amajority of nucleotides that are incapable of forming standardWatson-Crick base pairs, particularly with other nucleotides within thesame primer.

As used herein, the term “complementary” or “complement(s)” may refer tonucleic acid(s) that are substantially complementary, as may be assessedby the same nucleotide comparison set forth above. The term“substantially complementary” may refer to a nucleic acid comprising atleast one sequence of consecutive nucleobases, or semiconsecutivenucleobases if one or more nucleobase moieties are not present in themolecule, are capable of hybridizing to at least one nucleic acid strandor duplex even if less than all nucleobases do not base pair with acounterpart nucleobase. In certain embodiments, a “substantiallycomplementary” nucleic acid contains at least one sequence in whichabout 70%, about 71%, about 72%, about 73%, about 74%, about 75%, about76%, about 77%, about 77%, about 78%, about 79%, about 80%, about 81%,about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%,about 95%, about 96%, about 97%, about 98%, about 99%, to about 100%,and any range therein, of the nucleobase sequence is capable ofbase-pairing with at least one single or double stranded nucleic acidmolecule during hybridization. In certain embodiments, the term“substantially complementary” refers to at least one nucleic acid thatmay hybridize to at least one nucleic acid strand or duplex in stringentconditions. In certain embodiments, a “partially complementary” nucleicacid comprises at least one sequence that may hybridize in lowstringency conditions to at least one single or double stranded nucleicacid, or contains at least one sequence in which less than about 70% ofthe nucleobase sequence is capable of base-pairing with at least onesingle or double stranded nucleic acid molecule during hybridization.

As used herein, “hybridization”, “hybridizes” or “capable ofhybridizing” is understood to mean the forming of a double or triplestranded molecule or a molecule with partial double or triple strandednature. The term “hybridization”, “hybridize(s)” or “capable ofhybridizing” encompasses the terms “stringent condition(s)” or “highstringency” and the terms “low stringency” or “low stringencycondition(s).”

As used herein “stringent condition(s)” or “high stringency” are thosethat allow hybridization between or within one or more nucleic acidstrand(s) containing complementary sequence(s), but precludeshybridization of random sequences. Stringent conditions tolerate little,if any, mismatch between a nucleic acid and a target strand. Suchconditions are well known to those of ordinary skill in the art, and arepreferred for applications requiring high selectivity. Non-limitingapplications include isolating at least one nucleic acid, such as a geneor nucleic acid segment thereof, or detecting at least one specific mRNAtranscript or nucleic acid segment thereof, and the like.

Stringent conditions may comprise low salt and/or high temperatureconditions, such as provided by about 0.02 M to about 0.15 M NaCl attemperatures of about 50° C. to about 70° C. It is understood that thetemperature and ionic strength of a desired stringency are determined inpart by the length of the particular nucleic acid(s), the length andnucleobase content of the target sequence(s), the charge composition ofthe nucleic acid(s), and to the presence of formamide,tetramethylammonium chloride or other solvent(s) in the hybridizationmixture. It is generally appreciated that conditions may be renderedmore stringent, such as, for example, the addition of increasing amountsof formamide.

It is also understood that these ranges, compositions and conditions forhybridization are mentioned by way of non-limiting example only, andthat the desired stringency for a particular hybridization reaction isoften determined empirically by comparison to one or more positive ornegative controls. Depending on the application envisioned, it ispreferred to employ varying conditions of hybridization to achievevarying degrees of selectivity of the nucleic acid(s) towards targetsequence(s). In a non-limiting example, identification or isolation ofrelated target nucleic acid(s) that do not hybridize to a nucleic acidunder stringent conditions may be achieved by hybridization at lowtemperature and/or high ionic strength. Such conditions are termed “lowstringency” or “low stringency conditions”, and non-limiting examples oflow stringency include hybridization performed at about 0.15 M to about0.9 M NaCl at a temperature range of about 20° C. to about 50° C. Ofcourse, it is within the skill of one in the art to further modify thelow or high stringency conditions to suite a particular application.

As used herein a “nucleobase” refers to a naturally occurringheterocyclic base, such as A, T, G, C or U (“naturally occurringnucleobase(s)”), found in at least one naturally occurring nucleic acid(i.e. DNA and RNA), and their naturally or non-naturally occurringchimeras, derivatives, and analogs. Non-limiting examples of nucleobasesinclude purines and pyrimidines, as well as derivatives and analogsthereof, which generally can form one or more hydrogen bonds (“anneal”or “hybridize”) with at least one naturally occurring nucleobase in amanner that may substitute for naturally occurring nucleobase pairing(e.g. the hydrogen bonding between A and T, G and C, and A and U).

As used herein, a “nucleotide” refers to a nucleoside further comprisinga “backbone moiety” generally used for the covalent attachment of one ormore nucleotides to another molecule or to each other to form one ormore nucleic acids. The “backbone moiety” in naturally occurringnucleotides typically comprises a phosphorus moiety, which is covalentlyattached to a 5-carbon sugar. The attachment of the backbone moietytypically occurs at either the 3′- or 5′-position of the 5-carbon sugar.However, other types of attachments are known in the art, particularlywhen the nucleotide comprises derivatives or mimics of a naturallyoccurring 5-carbon sugar or phosphorus moiety, and non-limiting examplesare described herein.

IV. Amplification of Nucleic Acids

Nucleic acids useful as templates for amplification are generated bymethods described herein. In a specific embodiment, the DNA moleculefrom which the methods generate the nucleic acids for amplification maybe isolated from cells, tissues or other samples according to standardmethodologies (Sambrook et al., 1989).

The term “primer,” as used herein, is meant to encompass any nucleicacid that is capable of priming the synthesis of a nascent nucleic acidin a template-dependent process. Typically, primers are oligonucleotidesfrom ten to twenty and/or thirty base pairs in length, but longersequences can be employed. Primers may be provided in double-strandedand/or single-stranded form, although the single-stranded form ispreferred.

Pairs of primers designed to selectively hybridize to nucleic acids arecontacted with the template nucleic acid under conditions that permitselective hybridization. Depending upon the desired application, highstringency hybridization conditions may be selected that will only allowhybridization to sequences that are completely complementary to theprimers. In other embodiments, hybridization may occur under reducedstringency to allow for amplification of nucleic acids containing one ormore mismatches with the primer sequences. Once hybridized, thetemplate-primer complex is contacted with one or more enzymes thatfacilitate template-dependent nucleic acid synthesis. Multiple rounds ofamplification, also referred to as “cycles,” are conducted until asufficient amount of amplification product is produced.

The amplification product may be detected or quantified. In certainapplications, the detection may be performed by visual means.Alternatively, the detection may involve indirect identification of theproduct via chemiluminescence, radioactive scintigraphy of incorporatedradiolabel or fluorescent label or even via a system using electricaland/or thermal impulse signals (Affymax technology).

A number of template dependent processes are available to amplify theoligonucleotide sequences present in a given template sample. One of thebest known amplification methods is the polymerase chain reaction(referred to as PCR™) which is described in detail in U.S. Pat. Nos.4,683,195, 4,683,202 and 4,800,159, and in Innis et al., 1990, each ofwhich is incorporated herein by reference in their entirety. Briefly,two synthetic oligonucleotide primers, which are complementary to tworegions of the template DNA (one for each strand) to be amplified, areadded to the template DNA (that need not be pure), in the presence ofexcess deoxynucleotides (dNTP's) and a thermostable polymerase, such as,for example, Taq (Thermus aquaticus) DNA polymerase. In a series(typically 30-35) of temperature cycles, the target DNA is repeatedlydenatured (around 95° C.), annealed to the primers (typically at 50-60°C.) and a daughter strand extended from the primers (72° C.). As thedaughter strands are created they act as templates in subsequent cycles.Thus, the template region between the two primers is amplifiedexponentially, rather than linearly.

A reverse transcriptase PCR™ amplification procedure may be performed toquantify the amount of mRNA amplified. Methods of reverse transcribingRNA into cDNA are well known and described in Sambrook et al., 1989.Alternative methods for reverse transcription utilize thermostable DNApolymerases. These methods are described in WO 90/07641. Polymerasechain reaction methodologies are well known in the art. Representativemethods of RT-PCR™ are described in U.S. Pat. No. 5,882,864.

A. LCR

Another method for amplification is the ligase chain reaction (“LCR”),disclosed in European Patent Application No. 320,308, incorporatedherein by reference. In LCR, two complementary probe pairs are prepared,and in the presence of the target sequence, each pair will bind toopposite complementary strands of the target such that they abut. In thepresence of a ligase, the two probe pairs will link to form a singleunit. By temperature cycling, as in PCR™, bound ligated units dissociatefrom the target and then serve as “target sequences” for ligation ofexcess probe pairs. U.S. Pat. No. 4,883,750, incorporated herein byreference, describes a method similar to LCR for binding probe pairs toa target sequence.

B. Qbeta Replicase

Qbeta Replicase, described in PCT Patent Application No. PCT/US87/00880,also may be used as still another amplification method in the presentinvention. In this method, a replicative sequence of RNA which has aregion complementary to that of a target is added to a sample in thepresence of an RNA polymerase. The polymerase will copy the replicativesequence which can then be detected and quantified

C. Isothermal Amplification

An isothermal amplification method, in which restriction endonucleasesand ligases are used to achieve the amplification of target moleculesthat contain nucleotide thiophosphates in one strand of a restrictionsite also may be useful in the amplification of nucleic acids in thepresent invention. Such an amplification method is described by Walkeret al. 1992, incorporated herein by reference.

D. Strand Displacement Amplification

Strand Displacement Amplification (SDA) is another method of carryingout isothermal amplification of nucleic acids which involves multiplerounds of strand displacement and synthesis, i.e., nick translation. Asimilar method, called Repair Chain Reaction (RCR), involves annealingseveral probes throughout a region targeted for amplification, followedby a repair reaction in which only two of the four bases are present.The other two bases can be added as biotinylated derivatives for easydetection. A similar approach is used in SDA.

E. Cyclic Probe Reaction

Target specific sequences can also be detected using a cyclic probereaction (CPR). In CPR, a probe having 3′ and 5′ sequences ofnon-specific DNA and a middle sequence of specific RNA is hybridized toDNA which is present in a sample. Upon hybridization, the reaction istreated with RNase H, and the products of the probe identified asdistinctive products which are released after digestion. The originaltemplate is annealed to another cycling probe and the reaction isrepeated.

F. Transcription-Based Amplification

Other nucleic acid amplification procedures include transcription-basedamplification systems (TAS), including nucleic acid sequence basedamplification (NASBA) and 3SR, Kwoh et al., 1989; PCT Patent ApplicationWO 88/10315, each incorporated herein by reference).

In NASBA, the nucleic acids can be prepared for amplification bystandard phenol/chloroform extraction, heat denaturation of a clinicalsample, treatment with lysis buffer and minispin columns for isolationof DNA and RNA or guanidinium chloride extraction of RNA. Theseamplification techniques involve annealing a primer which has targetspecific sequences. Following polymerization, DNA/RNA hybrids aredigested with RNase H while double stranded DNA molecules are heatdenatured again. In either case the single stranded DNA is made fullydouble stranded by addition of a second target specific primer, followedby polymerization. The double-stranded DNA molecules are then multiplytranscribed by an RNA polymerase, such as T7 or SP6. In an isothermalcyclic reaction, the RNAs are reverse transcribed into double strandedDNA, and transcribed once again with an RNA polymerase, such as T7 orSP6. The resulting products, whether truncated or complete, indicatetarget specific sequences.

G. Rolling Circle Amplification

Rolling circle amplification (U.S. Pat. No. 5,648,245) is a method toincrease the effectiveness of the strand displacement reaction by usinga circular template. The polymerase, which does not have a 5′exonuclease activity, makes multiple copies of the information on thecircular template as it makes multiple continuous cycles around thetemplate. The length of the product is very large—typically too large tobe directly sequenced. Additional amplification is achieved if a secondstrand displacement primer is added to the reaction using the firststrand displacement product as a template.

H. Other Amplification Methods

Other amplification methods, as described in British Patent ApplicationNo. GB 2,202,328, and in PCT Patent Application No. PCT/US89/01025, eachincorporated herein by reference, may be used in accordance with thepresent invention. In the former application, “modified” primers areused in a PCR™ like, template and enzyme dependent synthesis. Theprimers may be modified by labeling with a capture moiety (e.g., biotin)and/or a detector moiety (e.g., enzyme). In the latter application, anexcess of labeled probes are added to a sample. In the presence of thetarget sequence, the probe binds and is cleaved catalytically. Aftercleavage, the target sequence is released intact to be bound by excessprobe. Cleavage of the labeled probe signals the presence of the targetsequence.

Miller et al., PCT Patent Application WO 89/06700 (incorporated hereinby reference) disclose a nucleic acid sequence amplification schemebased on the hybridization of a promoter/primer sequence to a targetsingle-stranded DNA (“ssDNA”) followed by transcription of many RNAcopies of the sequence. This scheme is not cyclic, i.e., new templatesare not produced from the resultant RNA transcripts.

Other suitable amplification methods include “RACE” and “one-sided PCR™”(Frohman, 1990; Ohara et al., 1989, each herein incorporated byreference). Methods based on ligation of two (or more) oligonucleotidesin the presence of nucleic acid having the sequence of the resulting“di-oligonucleotide”, thereby amplifying the di-oligonucleotide, alsomay be used in the amplification step of the present invention, Wu etal., 1989, incorporated herein by reference).

V. Enzymes

Enzymes that may be used in conjunction with the invention includenucleic acid modifying enzymes listed in the following tables.

TABLE I POLYMERASES AND REVERSE TRANSCRIPTASES Thermostable DNAPolymerases: OmniBase ™ Sequencing Enzyme Pfu DNA Polymerase Taq DNAPolymerase Taq DNA Polymerase, Sequencing Grade TaqBead ™ Hot StartPolymerase AmpliTaq Gold Tfl DNA Polymerase Tli DNA Polymerase Tth DNAPolymerase DNA Polymerases: DNA Polymerase I, Klenow Fragment,Exonuclease Minus DNA Polymerase I DNA Polymerase I Large (Klenow)Fragment Terminal Deoxynucleotidyl Transferase T4 DNA Polymerase ReverseTranscriptases: AMV Reverse Transcriptase MMLV Reverse Transcriptase HIVReverse Transcriptase

TABLE II DNA/RNA MODIFYING ENZYMES Ligases: T4 DNA Ligase Kinases T4Polynucleotide Kinase

VI. DNA Polymerases

In a preferred embodiment, a DNA polymerase is used in methods of thepresent invention. In some embodiments, it is envisioned that themethods of the invention could be carried out with one or more enzymeswhere multiple enzymes combine to carry out the function of a single DNApolymerase molecule retaining 5′-3′ exonuclease activities. Effectivepolymerases that retain 5′-3′ exonuclease activity include, for example,E. coli DNA polymerase I, Taq DNA polymerase, S. pneumoniae DNApolymerase I, Tfl DNA polymerase, D. radiodurans DNA polymerase I, TthDNA polymerase, Tth XL DNA polymerase, M. tuberculosis DNA polymerase I,M. thermoautotrophicum DNA polymerase I, Herpes simplex-1 DNApolymerase, E. coli DNA polymerase I Klenow fragment, Vent DNApolymerase, thermosequenase and wild-type or modified T7 DNApolymerases. In preferred embodiments, the effective polymerase is E.coli DNA polymerase I, Klenow, or Taq DNA polymerase, or MMLV reversetranscriptase.

Where a break in the substantially double stranded nucleic acid templateis a gap of at least a base or nucleotide in length that comprises, oris reacted to comprise, a 3′ hydroxyl group, the range of effectivepolymerases that may be used is even broader. In such aspects, theeffective polymerase may be, for example, E. coli DNA polymerase I, TaqDNA polymerase, S. pneumoniae DNA polymerase I, Tfl DNA polymerase, D.radiodurans DNA polymerase I, Tth DNA polymerase, Tth XL DNA polymerase,M. tuberculosis DNA polymerase I, M. thermoautotrophicum DNA polymeraseI, Herpes simplex-1 DNA polymerase, E. coli DNA polymerase I Klenowfragment, T4 DNA polymerase, Vent DNA polymerase, thermosequenase or awild-type or modified T7 DNA polymerase. In preferred aspects, theeffective polymerase is E. coli DNA polymerase I, M. tuberculosis DNApolymerase I, Taq DNA polymerase, or T4 DNA polymerase.

VII. Hybridization

Depending on the application envisioned, one would desire to employvarying conditions of hybridization to achieve varying degrees ofselectivity of the probe or primers for the target sequence, such as inthe adaptor. For applications requiring high selectivity, one willtypically desire to employ relatively high stringency conditions to formthe hybrids. For example, relatively low salt and/or high temperatureconditions, such as provided by about 0.02 M to about 0.10 M NaCl attemperatures of about 50° C. to about 70° C. Such high stringencyconditions tolerate little, if any, mismatch between the probe orprimers and the template or target strand and would be particularlysuitable for isolating specific genes or for detecting specific mRNAtranscripts. It is generally appreciated that conditions can be renderedmore stringent by the addition of increasing amounts of formamide.

Conditions may be rendered less stringent by increasing saltconcentration and/or decreasing temperature. For example, a mediumstringency condition could be provided by about 0.1 to 0.25 M NaCl attemperatures of about 37° C. to about 55° C., while a low stringencycondition could be provided by about 0.15 M to about 0.9 M salt, attemperatures ranging from about 20° C. to about 55° C. Hybridizationconditions can be readily manipulated depending on the desired results.

In other embodiments, hybridization may be achieved under conditions of,for example, 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 35 mM MgCl₂, 1.0 mMdithiothreitol, at temperatures between approximately 20° C. to about37° C. Other hybridization conditions utilized could includeapproximately 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl₂, attemperatures ranging from approximately 40° C. to about 72° C.

EXAMPLES

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples that follow representtechniques discovered by the inventors to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Example 1: Design of Degenerate Pyrimidine Primers and Analysis ofSelf-Priming and Extension

Pyrimidine primers comprising a constant 18 base sequence, followed by10 random pyrimidines and between 0 and 6 completely random bases at the3′ end (Table III, primers 1-7), are compared for their ability to selfprime and to extend a model template oligonucleotide.

TABLE III OLIGONUCLEOTIDE SEQUENCES No Code Sequence 5′-3′ *  1. YCCTTTCTCTCCCTTCTCTYYYYYYYYYY (SEQ ID NO: 11)  2. YNCCTTTCTCTCCCTTCTCTYYYYYYYYYYN (SEQ ID NO: 12)  3. Y(N)₂CCTTTCTCTCCCTTCTCTYYYYYYYYYYNN (SEQ ID NO: 13)  4. Y(N)₃CCTTTCTCTCCCTTCTCTYYYYYYYYYYNNN (SEQ ID NO: 14)  5. Y(N)₄CCTTTCTCTCCCTTCTCTYYYYYYYYYNNNN (SEQ ID NO: 15)  6. Y(N)₅CCTTTCTCTCCCTTCTCTYYYYYYYYYYNNNNN (SEQ ID NO: 16)  7. Y(N)₆CCTTTCTCTCCCTTCTCTYYYYYYYYYYNNNNNN (SEQ ID NO: 17)  8 Y_(U)CCTTTCTCTCCCTTCTCT (SEQ ID NO: 18)  9. TemplateGTAATACGACTCACTATAGGRRRRRRRRRR (SEQ ID NO: 19) 10. R(N)₂AGAGAAGGGAGAGAAAGGRRRRRRRRRRNN (SEQ ID NO: 20) 11. R_(U)AGAGAAGGGAGAGAAAGG (SEQ ID NO: 21) 12. M(N)₂CCAAACACACCCAACACAMMMMMMMMMMNN (SEQ ID NO: 22) 13. M_(U)CCAAACACACCCAACACA (SEQ ID NO: 23) 14. K(N)₂TGTGTTGGGTGTGTTTGGKKKKKKKKKKNN (SEQ ID NO: 24) 15. KTGTGTTGGGTGTGTTTGGKKKKKKKKKK (SEQ ID NO: 25) 16. K_(U)TGTGTTGGGTGTGTTTGG (SEQ ID NO: 26) 17 T7(N)₆ GTAATACGACTCACTATAGGNNNNNN(SEQ ID NO: 27) 18. T7 GTAATACGACTCACTATAGG (SEQ ID NO: 28) 19. K(T20)TGTGTTGGGTGTGTTTGGTTTTTTTTTTTTTTTTTTTT (SEQ ID NO: 29) * Random basesdefinitions: Y = C or T; R = A or G; M = A or C; K = G or T

The model template oligonucleotide (Table III, Oligonucleotide 9) wascomprised of T7 promoter sequence followed by 10 random purine bases atits 3′-terminus. The reaction mixture contained 1× ThermoPol reactionbuffer (NEB), 4 units of Bst DNA Polymerase Large Fragment (NEB), 200 uMdNTPS, 350 nM template oligo 9, and 3.5 or 35 μM of degeneratepyrimidine primers Y and YN (Table III, primers 1 to 7) in a finalvolume of 25 Controls comprising no dNTPs are also included for each Yor YN primer. Samples were incubated for 5 min or 15 min at 45° C. andstopped by adding 2 μl of 0.5 M EDTA. Aliquots of the reactions wereanalyzed on 10% TB-urea denaturing polyacrylamide gels (Invitrogen)after staining with SybrGold dye (Molecular Probes). FIG. 3 shows theresult of the comparison experiment. No evidence of self-priming wasfound with primers having up to 3 random bases at their 3′-end whenapplied at 35 μM concentration after 5 min incubation with Bstpolymerase and dNTPs at 45° C. (FIG. 3A). In contrast, in the samplescontaining template oligonucleotide, a new band corresponding toextension products was observed at both 35 μM and 3.5 μM primersconcentration (FIG. 3B). In a separate experiment degenerate pyrimidineprimers having up to six random bases at the 3′-end were analyzed fortheir ability to self-prime (FIG. 3C). After 15 min of incubation withBst polymerase, no extension products were observed with primers having3 random bases or less (FIG. 3C, lanes 1-3), whereas the primers withhigher complexity (N3 and above) showed progressively increasing amountof extension products (FIG. 3C, lanes 4-6). Control samples incubatedwith Bst polymerase but no dNTPs, showed no extension products (FIG. 3C,lanes 7-12).

Example 2: Comparison of Different Degenerate Pyrimidine Primers Used inthe Library Synthesis with Klenow Exo− Fragment of DNA Polymerase-I andSubsequent Whole Genome Amplification

Human lymphocyte genomic DNA isolated by standard procedures wasrandomly fragmented in TE buffer to an average size of 1.5 Kb using theHydro Shear™ device (Gene Machines; Palo Alto, Calif.). The reactionmixture contained 50 ng of fragmented DNA in 1× EcoPol buffer (NEB), 200μM of each dNTP, 360 ng of Single Stranded DNA Binding Protein (USB),500 nM of known Y_(U) primer (Table III, primer 8), and 1 μM ofdegenerate pyrimidine primers with 0 to 6 random 3′ bases (Table III,primers 1-7) or 1 μM of T7 primer with six random N bases at the 3′ end(Table III, T7(N)₆ primer 16,) in a final volume of 25 μl. After adenaturing step of 2 min at 95° C., the samples were cooled to 16° C.,and the reaction was initiated by adding 5 units of Klenow enzyme thatlacks 3′-5′ exonuclease activity (NEB). WGA library synthesis wascarried out in a three-step protocol for 10 min at 16° C., 10 min at 24°C., and 15 min at 37° C. Reactions were stopped with 1 μl of 250 mM EDTA(pH 8.0), and samples were heated for 3 min at 95° C. Aliquots wereanalyzed on a 1% agarose gel after staining with EtBr (FIG. 4). FIG. 4shows that under the conditions used in the assay, primer dimers wereformed only when using YN primers with 3 or more completely random 3′bases. The amount of dimers increased progressively with an increase inthe number of random bases (FIG. 4, lanes 4-7). In contrast, no primerdimers were formed when using primers with up to 2 completely random 3′bases (FIG. 4, lanes 1-3). When a primer containing a constant T7promoter sequence (which contains both purines and pyrimidines) andcompletely random hexamers at its 3′ end was used (Table III, primer16), excessive amount of dimers was generated (FIG. 4, lane 8).

Aliquots of the library reactions corresponding to 5 ng of input DNAwere further amplified by real-time PCR. The PCR reaction mixturecontained: 1× Titanium Taq reaction buffer (Clontech), 200 μM each dNTP,100,000× dilutions of fluorescein and SybrGold I (Molecular Probes), 1μM known Y_(U) primer (or in the case of degenerate T7(N)₆ primers,known primer T7 (Table III, primer 17), 5 units of Titanium Taqpolymerase (Clontech), and 3 μl aliquots (approximately 5 ng inputgenomic DNA) of the Klenow library synthesis reactions in a final volumeof 50 μl. Reactions were carried out for 18 cycles at 94° C. for 15 secand 65° C. for 2 min on I-Cycler™ real-time PCR instruments (Bio-Rad).FIG. 5 shows the chromatograms of the real-time PCR. All degeneratepyrimidine primers showed similar efficiency of amplification with asignal corresponding to 50% of the maximum centered around cycle 9,whereas the T7 sequence with random hexamers at the 3′ end (Table III,primer 16) is more than an order of magnitude less efficient (4 cyclesright shifted) due to formation of excessive primer dimers (see FIG. 5,lane 8).

Representation analysis of the samples prepared with pyrimidine primerswith 0 to 6 random 3′ bases was conducted using a panel of 30 humangenomic STS markers (Table IV, STS markers 1-6, 8-10, 12, 14, 16, 19,20, 23, 26, 29-31, 35, 36, 38, 40, 41, 43, 44, 46, 47, and 49)

TABLE IV EXEMPLARY HUMAN STS MARKERS USED FOR REPRESENTATION ANALYSIS BYQUANTITATIVE REAL-TIME PCR No * UniSTS Database Name**  1 RH18158  2SHGC-100484  3 SHGC-82883  4 SHGC-149956  5 SHGC-146783  6 SHGC-102934 8 csnpmnat1-pcr1-1  9 stSG62224 10 SHGC-142305 12 SHGC-80958 13SHGC-74059 14 SHGC-83724 16 SHGC-145896 19 SHGC-155401 20csnpharp-pcr2-3 22 stb39J12.sp6 23 SHGC-149127 26 949_F_8Left 29SHGC-148759 30 SHGC-154046 31 WI-19180 35 SHGC-146602 36 SHGC-130262 38SHGC-130314 40 SHGC-147491 41 stSG53466 42 SHGC-105883  42a GDB:533006 42b D19S1101 43 SHGC-79237 44 SHGC-153761 46 stSG50529 47 SHGC-13219949 stSG49452 51 SGC32543 52 SHGC-2457 53 stSG53950 54 stSG43297 55SHGC-81536 58 stSG48086 60 stSG62388 62 stSG50542 63 stSG44393 66SHGC-9458 67 SHGC-5506 68 SHGC-153324 69 stSG53179 70 sts-X16316 71stSG51782 72 stSG48421 74 stGDB:442878 76 WI-6290 77 T94852 79SHGC-11640 80 H58497 81 stSG34953 82 KIAA0108 83 Y00805 84 sts-W93373 85stSG45551  85a Cda0ge01  85b RH18026 86 U34806 88 SHGC-12728 89SHGC-10570 91 stSG52141 92 SHGC-58853 94 SHGC-36464 96 stSG8946 97SHGC-10187 99 WI-13668 103  stSG49584 104  M55047 105  SHGC-102231 106 stSG60168 107  stSG50880 108  stSG39197 110  sts-AA035504 111  SGC35140113  stSG53011 114  sts-R44709 116  SHGC-149512 117  stSG55021 118 SHGC-79529 119  KIAA0181 119a GDB:314031 119b RH28558 120  SHGC-105119121  SHGC-79242 122  SHGC-170363 123  stSG50637 126  RH69540 130 GDB:181552 133  1770 134  1314 135  SHGC-104164 136  SHGC-101034 137 stSG62239 138  stSG60144 139  stSG58407 140  stSG58405 141  sts-T50718144  SHGC-17057 145  sts-N90764 152  SHGC-132991 154  SHGC-57595 AluYb8 * Omitted sequential numbers indicate dropped STS sequences that didnot amplify well in quantitative RT-PCR **Unique names of STS markersequences are from the National Center for Biotechnology InformationUniSTS database. Sequences of the STS regions as well as the forward andbackward primers used in quantitative real-time PCR can be found in theUniSTS database at the National Center for Biotechnology Information'swebsite.

The material amplified by PCR with the known Y_(U) primer was purifiedwith Qiaquick filters (Qiagen), and 10 ng aliquots were analyzed inreal-time PCR. Reactions were carried out for 45 cycles at 94° C. for 15sec and 68° C. for 1 min on an I-Cycler (Bio-Rad), as described above,in a 25 μl volume. Standards corresponding to 10, 1, and 0.2 ng offragmented DNA were used for each STS, quantities were calculated bystandard curve fit for each STS (I-Cycler software, Bio-Rad) and wereplotted as frequency histograms (FIG. 6). Of all pyrimidine primerstested, Y(N)₂ supported the most uniform whole genome amplification(FIG. 6A) with Klenow fragment of DNA polymerase I, yet produced limitedamount of primer dimers (FIG. 3 and FIG. 4). Eighty three percent of theSTS markers analyzed after whole genome amplification with Y(N)₂ primerwere within a factor of 2 times the mean and 90% within a factor of 3times the mean, whereas on average these numbers were in the range of 63to 70% and 73 to 80% respectively for all other YN-primers analyzed.

Example 3: Whole Genome Amplification of Thermally Fragmented GenomicDNA Converted into an Amplifiable DNA Library Using Klenow Exo− Fragmentof DNA Polymerase-I or Sequenase Version-2 and Degenerate Primers Y(N)₂

Human lymphocyte genomic DNA isolated by standard procedures wasrandomly fragmented in TE-L buffer (10 mM Tris, 0.1 mM EDTA, pH 7.5) byheating at 95° C. for 5 min. The reaction mixture contained 100 ng ofthermally fragmented DNA in 1× EcoPol buffer (NEB) or 1× Sequenasebuffer (USB), 200 μM of each dNTP, 360 ng of Single Stranded DNA BindingProtein (USB), 200 nM of known Y_(U) primer (Table III, primer 8), and500 nM of degenerate Y(N)₂ primer (Table III, primer 3) in a finalvolume of 25 μl. After a denaturing step of 2 min at 95° C., the sampleswere cooled to 16° C., and the reaction initiated by adding 2.5 units or6.5 units of Klenow Exo⁻ polymerase (NEB) or Sequenase version 2 (USB),respectively. WGA library synthesis was carried out in a three-stepprotocol for 10 min at 16° C., 10 min at 24° C., and 12 min at 37° C.Reactions were stopped with 1 μl of 500 mM EDTA (pH 8.0), and sampleswere heated for 3 min at 75° C. Aliquots of the library synthesisreactions corresponding to 5 ng of input DNA were further amplified byreal-time PCR. The PCR reaction mixture contained: 1× Titanium Taqreaction buffer (Clontech), 200 uM each dNTP, 100,000× dilutions offluorescein and SybrGreen I (Molecular Probes) 1 uM known Y_(U) primer(or in the case of random T7(N)₆ primers, known T7 (primer 18), 5 unitsof Titanium Taq polymerase (Clontech), and a volume of the librarysynthesis reaction corresponding to 5 ng of the input genomic DNA in afinal volume of 50 μl. Reactions were carried out for 17 cycles at 94°C. for 15 sec and 65° C. for 2 min on an I-Cycler real-time PCRinstrument (Bio-Rad). FIG. 7 shows the chromatograms of the real-timePCR. Sequenase version 2 showed an order of magnitude higher efficiencyas compared to Klenow Exo⁻ polymerase at both concentrations tested.Aliquots of the PCR amplification reactions were analyzed on a 1%agarose gel after staining with EtBr. Sequenase synthesis yieldedamplicons of larger average size compared to Klenow Exo⁻ polymerase(FIG. 8). Representation analysis of the PCR amplified librariesgenerated with Sequenase or Klenow Exo-polymerases was done using apanel of 33 human genomic STS markers (Table IV, STS markers 1, 5, 6,14, 19, 22, 26, 38, 43, 46, 47, 52, 53, 54, 58, 60, 62, 63, 69, 72, 74,80, 81, 82, 85, 89, 91, 94, 96, 99, 104, 107, 108)

The material amplified by PCR with the known Y_(U) primer was purifiedwith Qiaquick filters (Qiagen), and 10 ng aliquots were analyzed inreal-time PCR. Reactions were carried out for 45 cycles at 94° C. for 15sec and 68° C. for 1 min on I-Cycler (Bio-Rad), as described above in a25 μl volume. Standards corresponding to 10, 1, and 0.2 ng of fragmentedgenomic DNA were used for each STS. Quantities were calculated bystandard curve fit for each STS (I-Cycler software, Bio-Rad), andplotted as frequency histograms (FIG. 9). Sequenase library preparationsresulted in a more representative amplification compared to Klenow Exo⁻with fewer outliers. Between 80 and 85% of the STS markers analyzedafter amplification of libraries prepared with Sequenase were within afactor of 2 times the mean value, whereas those analyzed afteramplification of libraries prepared with Klenow fragment of DNApolymerase I averaged 67%.

Example 4. Comparison of Degenerate Primers Y(N)₂, R(N)₂, M(N)₂ andK(N)₂ Comprised of Only Two Non-Complementary Bases and Containing TwoTruly Random Bases at their 3′ Terminus in their Efficiency of HumanWhole Genome Library Preparation and Amplification

Human lymphocyte genomic DNA isolated by standard procedures wasrandomly fragmented in TE-L buffer by heating at 95° C. for 4 min. Thereaction mixtures (one for each degenerate primer) contained 100 ng ofthermally fragmented DNA in 1× EcoPol buffer (NEB), 200 μM of each dNTP,and 1 μM of degenerate Y(N)₂, R(N)₂, M(N)₂, or K(N)₂ primers (Table III,primers 3, 10, 12, and 14) in a final volume of 24 After denaturing at95° C. for 2 min the samples were cooled to 16° C. and the librarysynthesis reaction was initiated by adding 1 μl (3 units) of Sequenaseversion 2 (USB Corporation). The reaction was carried out in athree-step protocol for 15 min at 16° C., 15 min at 24° C., and 15 minat 37° C. Reactions were stopped by adding 1 ul of 250 mM EDTA (pH 8.0)and samples were heated for 5 min at 75° C. Aliquots of the libraryreactions corresponding to 5 ng of input DNA were further amplified byquantitative real-time PCR. The PCR reaction mixture contained: 1×Titanium Taq reaction buffer (Clontech), 200 μM each dNTP, 100,000×dilutions of fluorescein and SybrGreen I (Molecular Probes) 1 uM knownY_(U), R_(U), M_(U), or K_(U) primer whose sequence is identical to theknown 5′ portion of the respective degenerate primer (Table III, primers8, 11, 13, and 16), 5 units of Titanium Taq polymerase (Clontech), and 5ng input genomic DNA equivalent of the library synthesis reactions in afinal volume of 50 ul. Amplifications were carried out for 16 cycles at94° C. for 15 sec and 65° C. for 2 min on the I-Cycler real-time PCRinstrument (Bio-Rad). FIG. 10 demonstrates that degenerate primercontaining guanine and thymidine (K(N)₂ primer) is priming mostefficiently of all primers tested. Also, both guanine containingdegenerate primers (R(N)₂ and K(N)₂) are more effective as compared tocytosine containing primers (M(N)₂ and Y(N)₂). These findings can beexplained by the fact that guanine and thymidine can participate innon-canonical base pairing more readily compared to the other two bases.Overall K(N)₂ primer was about an order of magnitude more effective ascompared to Y(N)₂ primer (FIG. 10). Representation analysis of the PCRamplified libraries generated with Sequenase was done using a panel of35 human genomic STS markers (Table IV, STS markers 40-44, 46, 47, 49,52, 54, 55, 58, 60, 62, 63, 66-70, 72, 74, 76, 77, 79, 80, 81-86, 88,and 89). The material amplified by PCR with known primers was purifiedwith Qiaquick filters (Qiagen) and 10 ng aliquots were analyzed inreal-time PCR. In addition, a combined sample containing 2.5 ng of eachindividual amplification reaction was run in parallel. Reactions werecarried out for 45 cycles at 94° C. for 15 sec and 68° C. for 1 min onI-Cycler (Bio-Rad) in a 25 μl volume. Standards corresponding to 10.1,and 0.2 ng of fragmented genomic DNA were used for each STS. Quantitieswere derived by standard curve fit for each STS (I-Cycler software,Bio-Rad) and plotted as frequency histograms. As shown on FIG. 11, theuse of K(N)₂ primer resulted in the most uniform and representative DNAamplification. In this study, 91% of the STS markers analyzed afteramplification with K(N)₂ primer were within 2 fold of the mean value,whereas for Y(N)₂, M(N)₂ and R(N)₂ primers they were 63%, 74%, and 83%,respectively.

Example 5. Comparison Between Different Modes of Incubation DuringPreparation of Whole Genome Libraries with Sequenase Version-2 and Y(N)2Degenerate Primers and Subsequent Representative Amplification of HumanDNA

Human lymphocyte genomic DNA isolated by standard procedures wasrandomly fragmented in TE-L buffer by heating at 95° C. for 4 min. Thereaction mixture contained 100 ng of thermally fragmented DNA in 1×EcoPol buffer (NEB), 200 μM of each dNTP, and 1 μM of degenerate Y(N)₂primer (Table III, primer 3) in a final volume of 25 μl. After adenaturing step of 2 min at 95° C., the samples were cooled to 16° C.,or 24° C. and the WGA library synthesis reactions were initiated byadding 3 units or of Sequenase version 2 (USB). The reactions werecarried out in three different protocols as follows: (i) isothermal 24°C. for 1 hour (ii) cycling between 16° C., 24° C., and 37° C. for 1 mineach for total of 19 cycles (total duration 1 hour), and (iii) threestep incubation protocol for 20 min at 16° C., 20 min at 24° C., and 20min at 37° C. Reactions were stopped with 1 μl of 250 mM EDTA (pH 8.0),and samples were heated for 5 min at 75° C. Aliquots of the librarysynthesis reactions corresponding to 5 ng of input DNA were furtheramplified by real-time PCR. The PCR reaction mixture contained: 1×Titanium Taq reaction buffer (Clontech), 200 μM each dNTP, 100,000×dilutions of fluorescein and SybrGreen I (Molecular Probes) 1 μM knownY_(U) primer (or Table III, primer 8), 5 units of Titanium Taqpolymerase (Clontech), and 5 ng input genomic DNA of the synthesisreactions in a final volume of 50 μl. Reactions were carried out for 17cycles at 94° C. for 15 sec and 65° C. for 2 min on I-Cycler real-timePCR instrument (Bio-Rad). FIG. 12 shows the chromatogram of thereal-time PCR. Isothermal incubation at 24° C. for 1 hour resulted inthe highest efficiency of amplification, followed by the 3-stepincubation protocol. The cycling incubation resulted in 2 cycles delayedkinetics as compared to isothermal incubation (FIG. 12). Representationanalysis of the samples amplified by PCR following library preparationwith Sequenase was done using a panel of 31 human genomic STS markers(Table IV, STS markers 40, 42-44, 46, 47, 49, 52, 54, 58, 60, 62, 66,67, 68, 71, 72, 74, 77, 79, 80-86, 88, and 89). The material amplifiedby PCR with the known Y_(U) primer was purified with Qiaquick filters(Qiagen), and 10 ng aliquots were analyzed in real-time PCR. Reactionswere carried out for 45 cycles at 94° C. for 15 sec and 68° C. for 1 minon I-Cycler (Bio-Rad), as described above in a 25 μl volume. Standardscorresponding to 10, 1, and 0.2 ng of fragmented genomic DNA were usedfor each STS. Quantities were derived by a standard curve fit for eachSTS (I-Cycler software, Bio-Rad) and plotted as frequency histograms(FIG. 13). As shown, the isothermal amplification resulted in a slightlybetter representation as compared to the other two incubation protocols.

Example 6. Titration of Self-Inert Degenerate Primer K(N)₂ Concentrationin Human Whole Genome Amplification Protocol with Sequenase

Human lymphocyte genomic DNA isolated by standard procedures wasrandomly fragmented in TE-L buffer by heating at 95° C. for 4 min. Thereaction mixture (25 ul) contained 100 ng of thermally fragmented DNA in1× EcoPol buffer (NEB), 200 μM of each dNTP, and 500 nM, 1 μM, 2 μM, 10μM, or 33 μM of the self-inert degenerate primer K(N)₂ containing G andT bases and 2 completely random bases at the 3′ end (Table III, primer14). After a denaturing step of 2 min at 95° C., the samples were cooledto 24° C., and the library synthesis reaction was initiated by theaddition of 3 units of Sequenase version 2 DNA polymerase (USB). WGAlibrary synthesis was carried out isothermally at 24° C. for 45 min.Reactions were stopped with 1 μl of 250 mM EDTA (pH 8.0), and sampleswere heated for 5 min at 75° C. Aliquots of the library synthesisreactions corresponding to 5 ng of the input DNA were further amplifiedby real-time PCR. The PCR reaction mixture contained: 1× Titanium Taqreaction buffer (Clontech), 200 μM each dNTP, 100,000× dilutions offluorescein and SybrGreen I (Molecular Probes) 1 uM known K_(U) primer(Table III, primer 16), 5 units of Titanium Taq polymerase (Clontech),and a volume of the library synthesis reaction corresponding to 5 ng ofinput genomic DNA in a final volume of 50 μl. Reactions were carried outfor 15 cycles at 94° C. for 15 sec and 65° C. for 2 min on I-Cyclerreal-time PCR instrument (Bio-Rad). FIG. 14 shows the chromatograms ofthe real-time PCR. The efficiency of amplification was similar atconcentrations of the self-inert degenerate primer K(N)₂ between 0.5 and2 μM. At 10 μM and at 33 μM, the amplification was inhibited (FIG. 14).Representation analysis of the samples amplified by PCR was done using apanel of 17 human STS markers (Table IV, STS markers: 40-44, 46, 47, 49,52, 54, 55, 58, 60, 62, 63, 66, and 67). The material amplified by PCRwith the known K_(U) primer was purified with Qiaquick filters (Qiagen),and 10 ng aliquots were analyzed in real-time PCR. Reactions werecarried out for 45 cycles at 94° C. for 15 sec and 68° C. for 1 min onI-Cycler (Bio-Rad), in a 25 μl volume. Standards corresponding to 10, 1,and 0.2 ng of fragmented genomic DNA were used for each STS. Quantitieswere calculated by standard curve fit for each STS (I-Cycler software,Bio-Rad), and plotted as distribution plot (FIG. 15). As shown, therepresentation of STS markers improved significantly by increasing theprimer K(N)₂ concentration from 0.5 μM to 2 μM. When 10 μM or 33 μM ofthe primer K(N)₂ was applied this resulted in a compromisedrepresentation of genomic markers (FIG. 15; data not shown for 33 μM).With primer concentrations between 0.5 and 2 μM, on average 91% of theSTS markers were within a factor of 2 fold the mean, whereas at 10 μMprimer the percentage was 82.

Example 7. Titration of the Input Amount of DNA in Human Whole GenomeAmplification with Degenerate Primer K(N)₂ and Sequenase

Human lymphocyte genomic DNA isolated by standard procedures wasrandomly fragmented in TE-L buffer by heating at 95° C. for 4 min. Thereaction mixtures contained 100 ng, 25 ng, 10 ng, or 5 ng of thermallyfragmented DNA (or just TE-L buffer as negative control) in 1× EcoPolbuffer (NEB), 200 μM of each dNTP, and 1 uM degenerate primer K(N)₂(Table III, primer 14) in a total volume of 15 μl. After a denaturingstep of 2 min at 95° C., the samples were cooled to 16° C., and thereaction initiated by adding 1.85 units of Sequenase version 2 DNApolymerase (USB). Library synthesis was done at 16° C. for 20 min 24° C.for 20 min, and 37° C. for 20 min. Reactions were stopped with 1 μl of83 mM EDTA (pH 8.0), and samples were heated for 5 min at 75° C.Aliquots of the synthesis reactions corresponding to 5 ng of input DNA(or in the case of 5 ng DNA the entire reaction mixture) were furtheramplified by real-time PCR. The PCR reaction mixture contained: 1×Titanium Taq reaction buffer (Clontech), 200 μM each dNTP, 100,000×dilutions of fluorescein and SybrGreen I (Molecular Probes) 1 μM knownK_(U) primer (Table III, primer 16), 5 units of Titanium Taq polymerase(Clontech), and 5 ng input genomic DNA of the library synthesisreactions in a final volume of 75 μl. Reactions were carried out for 14cycles at 94° C. for 15 sec and 65° C. for 2 min on I-Cycler real-timePCR instrument (Bio-Rad). FIG. 16 shows the chromatograms of thereal-time PCR. Representation analysis of the samples amplified by PCRwas done using a panel of 20 human STS markers (Table IV, STS markers:40, 42-44, 46, 47, 49, 52, 54, 55, 58, 60, 62, 63, 66-69, and 74). Thematerial amplified by PCR with known K_(U) primer was purified withQiaquick filters (Qiagen), and 10 ng aliquots were analyzed in real-timePCR. Reactions were carried out for 45 cycles at 94° C. for 15 sec and68° C. for 1 min on I-Cycler (Bio-Rad), in a 25 μl volume. Standardscorresponding to 10, 1, and 0.2 ng of fragmented genomic DNA were usedfor each STS. Quantitation was done by standard curve fit for each STS(I-Cycler software, Bio-Rad), and quantities were plotted as adistribution plot (FIG. 17). As shown, the representation of STS markerswas better when libraries were synthesized with less than 100 ng of DNA(FIG. 17). One hundred percent of the samples amplified from 25 ng orfrom 5 ng of genomic DNA were within a factor of 2 fold the mean,whereas samples amplified from 100 ng or 10 ng were on average 95%. Inthis example, the highest median value for the STS markers evaluated wasachieved using the 5 ng input template (FIG. 17).

Genomic libraries described herein provide a very efficient resource forhighly representative whole genome amplification. Size (200-2,000 bp)and a known priming (known sequence) site make them also very attractivefor such applications as DNA archiving, storing, retrieving andre-amplification. Multiple libraries can be immobilized and stored asmicro-arrays. Libraries covalently attached by one end to the bottom oftubes, micro-plates or magnetic beads can be used many times byreplicating immobilized amplicons, dissociating replicated molecules forimmediate use, and returning the original immobilized WGA library forcontinuing storage.

The structure of WGA amplicons can also be easily modified to introducea personal identification (ID) DNA tag to every genomic sample toprevent an unauthorized amplification and use of DNA. Only those whoknow the sequence of the ID tag will be able to amplify and analyzegenetic material. The tags can be useful for preventing genomiccross-contaminations when dealing with many clinical DNA samples

WGA libraries created from large bacterial clones (BACs, PACs, cosmids,etc) can be amplified and used to produce genomic micro-arrays.

The examples presented below describe processes that can enhance theoutlined applications of the WGA libraries.

Example 8. Incorporation of Individual Identification DNA Tags by WholeGenome Amplification; Recovery of the Individual WGA Libraries from aMixture of Several WGA Libraries

This example describes two processes of tagging individual WGA library(ies) with the DNA identification sequence (ID) for the purpose ofsubsequent recovery of this library from the mixture containing otherWGA libraries. Such a situation can occur intentionally or unavoidably,such as when manipulating or storing a very large number of WGA DNAsamples, or intentionally, such as when there is a need to preventunauthorized access to genetic information within the stored libraries.

Both processes involve known primers with known sequence U at the 3′ endand individual ID sequence tag at the 5′ end (FIG. 18). In the firstcase, the known primer is comprised of regular bases (A, T, G and C) andcan be replicated (FIG. 18A). In the second case, the known primer has anon-nucleotide linker L (for example, hexa ethylene glycole, HEG) andcannot be replicated (FIGS. 18B and 18C).

The process of tagging, mixing and recovery of 3 different WGA librariesusing replicable known primers is shown on FIG. 19. It comprises foursteps: 1) Three genomic DNA samples are converted into 3 WGA librariesusing the methods described earlier in the patent application; 2) ThreeWGA libraries are amplified using 3 individual replicable known primersT₁U, T₂U, and T₃U with the corresponding ID DNA tags T₁, T₂, and T₃ atthe 5′ end (FIG. 18A); 3) All three libraries are mixed together. Anyattempt to amplify and genotype the mix would result in a mixed pattern;and 4) The WGA libraries are segregated by PCR using individual IDprimers tags T₁, T₂, and T₃.

The process of tagging, mixing and recovery of 3 different WGA librariesusing non-replicable known primers is shown in FIG. 20. It comprisesfive steps: 1.) Three genomic DNA samples are converted into 3 WGAlibraries using the method described earlier in the patent application;2.) Three WGA libraries are amplified using 3 individual non-replicableknown primers T₁U, T₂U, and T₃U with the corresponding ID DNA tags T₁,T₂, and T₃ at the 5′ end (FIGS. 18B and 18C). The resulting productshave 5′ single stranded tails formed by ID regions of the primers; 3.)All three libraries are mixed together. Any attempt to amplify andgenotype the mix would result in a mixed pattern; 4.) The WGA librariesare segregated by hybridization of their 5′ tails to the complementaryoligonucleotides T₁*, T₂*, and T₃* immobilized on the solid support; and5.) The segregated libraries are amplified by PCR using known primer U.

The processes of tagging and recovery described above for genomiclibraries can be similarly applied to individual whole transcriptomelibraries.

Example 9. Incorporation of Poly-G and Poly-C Functional Tags intoWGA/WTA Libraries for Targeted DNA/RNA Amplification

WGA (or WTA) libraries prepared by the method of library synthesisdescribed in the invention may be modified or tagged to incorporatespecific sequences. The tagging reaction may incorporate a functionaltag. For example, the functional 5′ tag composed of poly cytosine mayserve to suppress library amplification with a terminal C10 sequence asa primer. Terminal complementary homo-polymeric G sequence can be addedto the 3′ ends of amplified WGA library by terminal deoxynucleotidyltransferase (FIG. 21A), by ligation of adapter containing poly-Csequence (FIG. 21B), or by DNA polymerization with a primercomplementary to the universal proximal sequence U with a 5′non-complementary poly-C tail (FIG. 21C). The C-tail may be from 8-30bases in length. In a preferred embodiment the length of C-tail is from10 to 12 bases.

As described in U.S. Patent Application 20030143599, hereby incorporatedby reference in its entirety, genomic DNA libraries flanked byhomo-polymeric tails consisting of G/C base paired double stranded DNA,or poly-G single stranded 3-extensions, are suppressed in theiramplification capacity with poly-C primer. This suppression is caused byreduced priming efficiency at poly G region because of formation ofalternative G-quartet-like secondary structure within this sequence andit does not depend on the size of DNA amplicons, in contrast to wellknown “suppression PCR” that results from “pan-like” double-strandedstructures formed by self-complementary adaptors and as a resultstrongly depends on the size of DNA fragments having been more prominentfor shortest amplicons (Siebert et al., 1995; U.S. Ser. No.00/575,9822A). This suppression effect is diminished for a targeted sitewhen balanced with a second site-specific primer, whereby amplificationof a plurality of fragments containing the unique priming site and theuniversal terminal sequence are amplified selectively using a specificprimer and a poly-C primer, for instance primer C₁₀. Those skilled inthe art will recognize that genomic complexity may dictate therequirement for sequential or nested amplifications to amplify a singlespecies of DNA to purity from a complex WGA library.

Example 10. WGA Libraries in the Microarray Format

For archiving purposes, for example, individual WGA libraries can beimmobilized, such as, for example, on a micro-array. Micro-array formatwould allow storing tens or even hundreds or thousands of immortalizedDNA samples on one small microchip and have fast automated access tothem. There are two principal ways that WGA libraries can be immobilizedto a micro-array surface: covalently and non-covalently. FIG. 22 showsthe process of covalent immobilization. It comprises 3 steps: Step 1.Hybridization of single stranded (denatured) WGA amplicons to the knownprimer-oligonucleotide U covalently attached to the solid support. Step2. Extension of the primer U and replication of the hybridized ampliconsby DNA polymerase. Step 3. Washing with 100 mM sodium hydroxide solutionand TE buffer. Non-covalent immobilization can be achieved by using WGAlibraries with affinity tags (like biotin) or DNA sequence tags at the5′ ends of amplicons. Biotin can be located at the 5′ end of the knownprimer U. Single stranded 5′ affinity and/or ID tags can be introducedby using non-replicable primers (FIG. 18 and FIG. 20). Biotinylatedlibraries can be immobilized through streptavidin covalently attached tothe surface of the micro-array. WGA libraries with a DNA sequence tag inthe form of a 5′ overhang can be hybridized to complementaryoligonucleotides covalently attached to the surface of the micro-array.Examples of both covalently and non-covalently arrayed libraries areshown in FIG. 23.

Example 11. Repeated Usage of Immobilized WGA Libraries

Covalently immobilized WGA libraries (or libraries immobilized throughthe biotin-streptavidin interaction) can be used repeatedly to producereplica libraries for whole genome amplification (FIG. 24). In thisexemplary, case the process comprises four steps: 1) Retrieval of theimmobilized library from the long term storage; 2) Replication of theimmobilized library using DNA polymerase and known primer U; 3)Dissociating replica molecules by sodium hydroxide, neutralization andamplification; and 4) Neutralization and return of the solid phaselibrary for a long term storage.

Example 12. Purification of the WGA Products Using a Non-ReplicablePrimer Affinity Tag and DNA Immobilization by Hybridization

For many applications, purity of the amplified DNA is critical. WGAlibraries with 5′ overhangs can be hybridized to complementaryoligonucleotides covalently attached to the surface of magnetic beads,tubes or micro-plates, washed with TE buffer or water to remove excessof dNTPs, buffer and DNA polymerase and then released by heating in asmall volume of TE buffer. For this purpose, the single stranded5′-affinity tag can be introduced by using a non-replicable primer (FIG.25).

Example 13. Comparison Between Whole Genome Amplification of LibrariesPrepared by Klenow Exo− Fragment of DNA Polymerase I with Self-InertPrimers and DOP-PCR Amplification

This example describes a side-by-side comparison between the wholegenome amplification described in the present invention and acommercially available kit for DOP-PCR amplification.

Human lymphocyte genomic DNA was isolated by standard protocol usingphenol-chloroform extraction.

For whole genome amplification with Klenow fragment of DNA polymerase I,samples containing 5 ng or 20 pg in 10 μl of TE-L buffer were randomlyfragmented by heating at 95° C. for 4 min. Samples were supplementedwith a reaction buffer containing final concentrations of 1× EcoPolbuffer (NEB), 200 μM of each dNTP, 1 μM degenerate K(N)₂ primer (TableIII, primer 14), and 15 ng/μl SSB protein (USB) in a total volume of 14μl. After a denaturing step of 2 min at 95° C., the samples were cooledto 24° C. and the library synthesis reactions were initiated by adding 5units (1 μl) of Klenow Exo− DNA polymerase (NEB).

After incubation for 60 min at 24° C., reactions were stopped by heatingat 75° C. for 5 min. The synthesis reactions were amplified by real-timePCR. The PCR reaction mixture contained: 1× Titanium Taq reaction buffer(Clontech), 200 μM of each dNTP, 100,000× dilutions of fluorescein andSybrGreen I (Molecular Probes) 1 μM universal K_(U) primer (Table III,primer 16), 5 units of Titanium Taq polymerase (Clontech), and theentire 15 μl library synthesis reactions in a final volume of 75Reactions were carried out at 94° C. for 15 sec and 65° C. for 2 min onI-Cycler real-time PCR instrument (Bio-Rad).

Amplifications by DOP-PCR were done using DOP PCR Master™ Kit purchasedfrom Roche Molecular Biochemicals (Catalog #1644963). Amplificationreactions were carried out under Protocol 2 of the manufacturer'smanual. Briefly, samples containing 5 ng or 20 pg of DNA (or controlsamples without DNA) in a 50 μl standard DOP PCR reaction mixturesupplemented with 100,000× dilutions of fluorescein and SybrGreen I(Molecular Probes) were amplified after denaturing for 5 min at 95° C.by cycling for 5 cycles at: 94° C. for 30 sec, 30° C. for 30 sec,ramping at 30° C. to 72° C. for 30 sec (1.4° C./sec), and 72° C. for 1.5min, followed by 45 cycles at: 94° C. for 30 sec, 62° C. for 30 sec, and72° C. for 1.5 min, and final extension at 72° C. for 7 min on I-Cyclerreal-time PCR instrument (Bio-Rad).

FIG. 26A shows the real-time PCR curves of the whole genomeamplification by Klenow Exo− and DOP-PCR. As shown, at both input DNAamounts, i.e. 5 ng and 20 pg, the whole genome amplification oflibraries prepared with Klenow fragment of DNA polymerase-I anddegenerate K(N)₂ primer was about 25 PCR cycles more efficient thanamplification with DOP-PCR. This result indicates that the methods inthe present invention are several orders of magnitude more sensitivethan DOP-PCR technology.

Representation analysis was performed using a panel of 16 random humangenome STS markers (Table IV, STS markers: 40, 4-44, 46, 47, 49, 52, 54,55, 58, 60, 62, 63, and 66). The material amplified by PCR withuniversal K_(U) primer was purified with Qiaquick filters (Qiagen), and10 ng aliquots were analyzed in real-time PCR. Reactions were carriedout for 45 cycles at 94° C. for 15 sec and 68° C. for 1 min on I-Cycler(Bio-Rad), in a 25 μl volume. Standards corresponding to 10, 1, and 0.2ng of fragmented genomic DNA were used for each STS. Quantitation was bystandard curve fit for each STS.

FIG. 26B shows a logarithmic distribution plot of the STS markersanalyzed derived from the real-time PCR standard curve fit. Thedistribution of all 16 genome markers was tighter and with significantlyreduced representation bias in PCR amplified whole genome librariesprepared by Klenow fragment of DNA polymerase I and degenerate K(N)₂primer as compared to DOP-PCR products. Also, the average quantity ofSTS markers by the proposed method was approximately an order ofmagnitude higher in the library amplified form 20 pg of genomic DNA(about 3 diploid genome equivalents) as compared to the DNA productprepared from 5 ng DNA (almost 1000 diploid genome equivalents) byDOP-PCR.

Taken together, these results demonstrate the superiority of the methodsin the present invention over the DOP-PCR technique (Telenius et al.,1992), both in terms of sensitivity and fidelity of genome sequencerepresentation.

Example 14: Library Generation and Whole Genome Amplification of DNAIsolated from Serum

This example describes the amplification of genomic DNA that has beenisolated from serum collected in serum separator tubes (SST). Blood wascollected into 8 ml vacutainer SST tubes. The serum tubes were allowedto sit at room temperature for 30′. The tubes were centrifuged for 10′at 1,000×G with minimal acceleration and braking. The serum wassubsequently transferred to a clean tube. Isolated serum samples may beused immediately for DNA extraction or stored at −20° C. prior to use.

DNA from 1 ml of serum was purified using the DRI ChargeSwitch BloodIsolation kit according to the manufacturer's protocols. The resultingDNA was precipitated using the pellet paint DNA precipitation kit(Novagen) according to the manufacturer's instructions and the samplewas resuspended in TE-Lo to a final volume of 30 ml for serum. Thequantity and concentration of DNA present in the sample was quantifiedby real-time PCR using Yb8 Alu primer pairs; Yb8F5′-CGAGGCGGGTGGATCATGAGGT-3′ (SEQ. ID NO:120), and Yb8R5′-TCTGTCGCCCAGGCCGGACT-3′ (SEQ. ID NO:121). Briefly, 25 ml reactionswere amplified for 40 cycles at 94° C. for 15 sec and 74° C. for 1 min.Standards corresponding to 10, 1, 0.1, 0.01, and 0.001 ng of genomic DNAwere used and the serum DNA quantities and concentrations werecalculated by standard curve fit (I-Cycler software, Bio-Rad).

DNA isolated from serum was randomly fragmented in TE-L buffer byheating at 95° C. for 4 min. The reaction mixture contained 10 ng ofthermally fragmented DNA in 1× EcoPol buffer (NEB), 200 μM of each dNTP,and 1 uM of degenerate K(N)₂ primer (Table III, primer 14) in a finalvolume of 15 After a denaturing step of 2 min at 95° C., the sampleswere cooled to 4° C. and the reaction initiated by adding 5 units KlenowExo− (NEB). WGA library synthesis was carried out by a three-stepincubation protocol for 20 min at 16° C., 20 min at 24° C., and 20 minat 37° C. Reactions were stopped by heating for 15 min at 75° C. andsubsequently cooling to 4° C. The entire library reaction was furtheramplified by real-time PCR. The PCR reaction mixture contained: 1×Titanium Taq reaction buffer (Clontech), 200 uM each dNTP, 10,000×dilutions of fluorescein and SybrGold I (Molecular Probes) 1 uM knownK_(U) primer (Table III, primer 15), 0.5× Titanium Taq polymerase(Clontech), and 10 ng input genomic DNA of the library reactions in afinal volume of Reactions were carried out for 17 cycles at 94° C. for15 sec and 65° C. for 2 min on an I-Cycler real-time PCR instrument(Bio-Rad). The amplification curve is illustrated in FIG. 27.

The amplified material was purified by Millipore Multiscreen PCR platesand quantified by optical density. Gel analysis of the amplifiedproducts indicated a size distribution (200 bp to 1.6 kb) similar to theoriginal serum DNA (FIG. 28A). Additionally, the amplified DNA wasanalyzed using real-time, quantitative PCR using a panel of humangenomic STS markers. The markers that make up the panel are listed inTable IV. Quantitative Real-Time PCR was performed using an I-CyclerReal-Time Detection System (Bio-Rad), as per the manufacturer'sdirections. Briefly, 25 μl reactions were amplified for 40 cycles at 94°C. for 15 sec and 65° C. for 1 min. Standards corresponding to 10, 1,and 0.2 ng of fragmented DNA were used for each STS, quantities werecalculated by standard curve fit for each STS (I-Cycler software,Bio-Rad) and were plotted as distributions. Quantitative real-time PCRof the WGA products from serum demonstrated that all 8 markers testedwere within a factor of 5 of the mean amplification. These resultsindicate that the representation of the original serum DNA is maintainedfollowing WGA. FIG. 28B is a scatterplot of the representation of thehuman genomic STS markers in the amplified DNA.

Example 15. Whole Genome Amplification of Single Human Cells andIndividual Hair Follicles from Libraries Prepared Using Self-InertDegenerate Primer K and Klenow Exo− Fragment of DNA Polymerase I

This example describes the whole genome amplification of total DNA fromsingle human blood cells, single sperm cells, and individual hairfollicles.

Three microliters of freshly drawn blood from a healthy female donorwere exponentially diluted in PCR tubes containing 27 μl dilution buffercomposed of 10 mM Tris-HCl, pH 7.5, 100 mM NaCl, and 0.5 mM EDTA to alevel of 1, 0.5, or 0.2 cells per assuming an average blood count of5×10³ nucleated cells per ml of blood. Similarly, 3 μl of ejaculate froma healthy donor were diluted to the same level assuming a sperm count of20,000 per μl of ejaculate. A single hair follicle from a healthy femaledonor was lysed as described below and then exponentially diluted inlysis buffer.

One microliter of the respective cell dilutions was mixed with 9 μl offreshly prepared lysis buffer containing 10 mM Tris-HCl, pH 7.5, 0.5 mMEDTA, 20 mM NaCl, 0.007% (w/v) sodium dodecyl sulfate (SDS), and 0.12mg/ml proteinase K (USB). In the case of a hair follicle, the folliclewas suspended in 10 μl of lysis buffer. The samples were incubated for 1hr at 50° C. to lyse the cells. The hair follicle sample was furthersequentially diluted with lysis buffer from 10² to 10⁶-fold and eachdilution was subjected to WGA library preparation.

Samples were heated at 99° C. for 4 min to inactivate the proteinase K,disintegrate the nucleoprotein, and thermally fragment the DNA. Thelibrary synthesis step was conducted in a reaction mixture containing 1×EcoPol buffer (NEB), 200 mM of each dNTP, 1 μM degenerate primer K(Table III, sequence ID 15), and 15 ng/μl SSB (USB) in a total volume of14 After a denaturing step of 2 min at 95° C., the samples were cooledto 24° C. and the reaction initiated by adding 5 units (1 μl) of KlenowExo− DNA polymerase (NEB). After incubation for 60 min at 24° C.reactions were stopped by heating at 75° C. for 5 min. The synthesizedlibraries were amplified by real-time PCR. The PCR reaction mixturecontained: 1× Titanium Taq reaction buffer (Clontech), 200 uM each dNTP,100,000× dilutions of fluorescein and SybrGreen I (Molecular Probes) 1uM universal K_(U) primer (Table III, primer 16), 5 units of TitaniumTaq polymerase (Clontech), and the entire 15 μl library synthesisreaction in a final volume of 75 In the case of hair follicle dilutionsa blank control without DNA was included. Redundant single cell samplesat different dilutions were amplified which served as auto-controls,i.e. one cell or no cells were amplified at the highest dilutions.Reactions were carried out at 94° C. for 15 sec and 65° C. for 2 min onI-Cycler real-time PCR instrument (Bio-Rad).

FIG. 29 shows amplification of single nucleated blood cells.Approximately 8 cycles separate the resulting amplification profilesbetween single cells and no cells, allowing clear distinction betweenthe presence or absence of a single blood cell.

Representation analysis of 5 single cell samples amplified by PCR wasdone using a panel of 16 human STS markers (Table IV, STS markers: 40,4-44, 46, 47, 49, 52, 54, 55, 58, 60, 62, 63, and 66). The materialamplified by PCR with universal K_(U) primer was purified with Qiaquickfilters (Qiagen), and 10 ng aliquots were analyzed in real-time PCR.Reactions were carried out for 45 cycles at 94° C. for 15 sec and 68° C.for 1 min on I-Cycler (Bio-Rad), in a 25 μl volume. Standardscorresponding to 10, 1, and 0.2 ng of fragmented genomic DNA were usedfor each STS. Quantitation was by standard curve fit for each STS. Toassess the effect of copy number on the amplification bias, ⅙ of thevolume of each individual single cell amplification reaction wascombined into a pooled sample. The pooled sample was analyzed for STSmarker representation as described above. Markers amplified at a levelof less than 0.2 ng of standard template were considered dropouts. TableV shows the number of dropout markers for 3 individual single cellamplifications, as compared to the pooled sample.

TABLE V STS markers amplification from whole genome amplified singleblood cells and a pool of six individually amplified single cellsMarkers Amplified % of total # of dropouts (n = 16) Single cell 10 37.5%Single cell 8 50.0% Single cell 10 37.5% Pooled sample 4 75.0%

The majority of genomic marker dropouts were random in individual singlecell amplification reactions. After pooling of individually amplifiedsingle cells, the number of dropouts decreased by approximately half(Table V).

FIG. 30 shows amplification of single sperm cells. The distance betweensamples with a single cell and samples without cells in this case wasonly about 2 cycles (not the expected approximately 6 cycles for ahaploid genome as compared to blood nucleated cells). In a specificembodiment, this difference is attributed to either inefficient lysis orthe presence of inhibitors of the amplification in sperm cells.Nonetheless, even with 2 cycles difference one can still distinguishbetween a single cell and no cell.

As shown on FIG. 31, exponential dilutions of a lysed hair follicleshowed a progressive shift of about 3.5-4 cycles as expected. Thehighest dilution of 1:1,000,000 amplified about two cycles before theblank control which when compared to purified genomic DNA corresponds toapproximately 2 pg of DNA. This demonstrates the potential of the methodfor forensic applications.

Example 16. Amplification of Single Human Chromosomes with DegenerateK(N)₀ Primer and Klenow Exo− Fragment of DNA Polymerase-I

This example describes the amplification of total DNA from single copyhuman chromosomes.

Single copies of derivative chromosomes from a lymphoblastoid cell linecarrying a translocation (11;12)(q21;p13.33) sorted in 5 μl of water ina 96 well microtiter plate were obtained from the Wellcome Trust SangerInstitute. Fourteen individual samples of each translocation derivativechromosome were lysed in freshly prepared lysis buffer containing 10 mMTris-HCl, pH 7.5, 0.5 mM EDTA, 20 mM NaCl, 0.007% (w/v) sodium dodecylsulfate (SDS), and 0.12 mg/ml proteinase K (USB) in a final volume of 10μl at 50° C. for 1 hr.

Samples were heated at 99° C. for 4 min to inactivate the proteinase K,disintegrate the nucleoprotein, and thermally fragment the DNA. Librarysynthesis was conducted in a reaction mixture containing 1× EcoPolbuffer (NEB), 200 μM of each dNTP, 1 mM degenerate K(N)₀ primer (TableIII, sequence ID 15), and 15 ng/μl SSB (USB) in a total volume of 14 μl.After a denaturing step of 2 min at 95° C., the samples were cooled to24° C. and the reaction initiated by adding 5 units (1 μl) of KlenowExo− DNA polymerase (NEB). After incubation for 60 min at 24° C.reactions were stopped by heating at 75° C. for 5 min. The librarysynthesis reactions were amplified by real-time PCR in a mixturecontained: 1× Titanium Taq reaction buffer (Clontech), 200 uM each dNTP,100,000× dilutions of fluorescein and SybrGreen I (Molecular Probes) 1uM universal K_(U) primer (Table III, primer 16), 5 units of TitaniumTaq polymerase (Clontech), and the entire 15 μl library synthesisreaction in a final volume of 75 μl. Blank controls without DNA werealso included. Reactions were carried out at 94° C. for 15 sec and 65°C. for 2 min on I-Cycler real-time PCR instrument (Bio-Rad).

FIG. 32 shows amplification of single copy human chromosomes.Approximately 4 cycles distance between single chromosomes and no DNAblank controls was observed.

Example 17. Application of Single-Cell WGA for Detection and Analysis ofAbnormal Cells

WGA amplified single-cell DNA can be used to analyze tissue cellheterogeneity on the genomic level. In the case of cancer diagnostics itwould facilitate the detection and statistical analysis of heterogeneityof cancer cells present in blood and/or biopsies. In the case ofprenatal diagnostics it would allow the development of non-invasiveapproaches based on the identification and genetic analysis of fetalcells isolated from blood and/or cervical smears. Analysis of DNA withinindividual cells could also facilitate the discovery of new cellmarkers, features, or properties that are usually hidden by thecomplexity and heterogeneity of the cell population.

Analysis of the amplified single-cell DNA can be performed in two ways.In the traditional approach shown on FIG. 33, amplified DNA samples areanalyzed one by one using hybridization to genomic micro-array, or anyother profiling tools such as PCR, sequencing, SNP genotyping,micro-satellite genotyping, etc. The method would include: 1.) Dispersalof the tissue into individual cells; 2.) Preparation and amplificationof individual (single-cell) WGA libraries; 3.) Analysis of individualsingle-cell genomic DNA by conventional methods. This approach can beuseful in situations when genome-wide assessment of individual cells isnecessary.

In the second approach shown on FIG. 34, amplified DNA samples arespotted on the membrane, glass, or any other solid support, and thenhybridized with a nucleic acid probe to detect the copy number of aparticular genomic region. The method would include: 1.) Dispersal ofthe tissue of interest into individual cells; 2.) Preparation andamplification of individual (single-cell) WGA libraries; 3.) Preparationof micro-arrays of individual (single-cell) WGA DNAs; 4.) Hybridizationof the single-cell DNA micro-arrays to a locus-specific probe; 5.) andQuantitative analysis of the cell heterogeneity. This approach can beespecially valuable in situations when only limited number of genomicregions should be analyzed in a large cell population.

Example 18. Application of Whole Genome Amplification for Detection andAnalysis of Gene Copy Number

WGA amplified DNA retains both sequence and copy number integrity duringlibrary synthesis and amplification. This feature of the librariesfacilitates the potential evaluation of cells or tissues suspected ofhaving undergone gene amplification events such as those observed inoncogenic transformation. Early detection of gene amplification eventsrequires the ability to examine the event in a few suspect cells orbiopsy material. This application is best illustrated with a set ofmodel samples from patients of known chromosomal aneuploidy in theX-chromosome as described in this example.

DNA from patients with XO, XX, and XXX served as template for WGAlibrary synthesis (kindly provided by Dr. Arul Chinnaiyan, University ofMichigan). DNA isolated by standard procedures was randomly fragmentedin TE-L buffer by heating at 95° C. for 4 min. The reaction mixturescontained 25 ng of thermally fragmented DNA (or just TE-L buffer asnegative control) in 1× EcoPol buffer (NEB), 200 μM of each dNTP, and 1uM degenerate K(N)₂ primer (Table III, primer 14) 15 ng/μl SSB (USB) ina total volume of 14 After a denaturing step of 2 min at 95° C., thesamples were cooled to 16° C., and the reaction initiated by adding 5units (1 μl) of Klenow exo− DNA polymerase (USB). WGA library synthesiswas done at 16° C. for 20 min 24° C. for 20 min, and 37° C. for 20 min.Reactions were stopped with 1 μl of 83 mM EDTA (pH 8.0), and sampleswere heated for 5 min at 75° C. Aliquots of the reactions correspondingto 5 ng of input DNA were amplified by real-time PCR. The PCR reactionmixture contained: 1× Titanium Taq reaction buffer (Clontech), 200 μMeach dNTP, 100,000× dilutions of fluorescein and SybrGreen I (MolecularProbes) 1 μM known K_(U) primer (Table III, primer 16), 5 units ofTitanium Taq polymerase (Clontech), and 5 ng input genomic DNA of thelibrary synthesis reactions in a final volume of 75 Reactions werecarried out for 14 cycles at 94° C. for 15 sec and 65° C. for 2 min onI-Cycler real-time PCR instrument (Bio-Rad).

For analysis, individual 5 ng aliquots of the library were compared tothe combined mixture reconstituting the entire 25 ng input templateusing X chromosome STS primer pairs (152 and 154 Table IV). The materialamplified by PCR with universal K_(U) primer was purified with Qiaquickfilters (Qiagen), and 10 ng aliquots were analyzed in real-time PCR.Reactions were carried out for 40 cycles at 94° C. for 15 sec and 68° C.for 1 min on I-Cycler (Bio-Rad), in a 25 μl volume.

FIG. 35 shows the normalized STS real-time PCR curves for each set ofprimers. Panels A and C display the clustering of the individual 5 ngaliquots amplified from a single 25 ng WGA library for samples with 1×,2×, and 3× chromosome copies. In each case the variation isapproximately +1-0.5 cycles. FIG. 35 panels B and D display how thevariation is averaged upon reconstitution of the individualamplifications. In each case the reconstituted mixture is tested intriplicate showing a full cycle shift in the doubling of the templatebetween 1× and 2× and the predicted approximately half cycle shift whena third copy (3×) is added in the case of trisomy for the X chromosome.

The precise copy number measurements shown here for WGA amplifiedlibraries exemplify the potential for clinical applications in geneamplification events. Combined with the ability to generate librariesfrom low amounts of template the invention can be used in cancer andprenatal diagnostics where DNA sample is frequently very limited.

Example 19. Whole Transcriptome Amplification Using Libraries Preparedfrom Poly A+ RNA by MMLV Reverse Transcriptase and Self-Inert DegeneratePrimers

This example describes application of the invention for the creation ofan amplifiable library faithfully representing the expression patternsof transcribed RNA within a cell or population of cells herein termed“Whole Transcriptome Amplification” (WTA).

Purified polyA+ RNA from EBV transformed human B lymphocytes, Raji cells(Clontech), served as input template for WTA library preparation. As inthe case of WGA protocol, WTA is performed in two steps: librarysynthesis and library amplification. Library synthesis involves similarself-inert degenerate primers (primers K), but a different DNApolymerase, specifically MMLV reverse transcriptase. It proceeds throughthe extension/strand displacement reactions similar to WGA, but requiresno fragmentation of the RNA template (although fragmentation can beapplied to reduce the average amplicon size if desireable). To improverepresentation of the 3′ termini of mRNA molecules primer K(T)₂₀ (TableIII primer 19) complementary to the polyA tails was also added. Toassemble the library synthesis reaction, primers were annealed to polyA+RNA templates. Annealing was facilitated by briefly heating the mixtureof 100 ng or 10 ng polyA+ RNA, primers K(N)₂ [1 μM] (Table III primer14) and K(T)₂₀ [200 nM] (Table III primer19) either in combination, orK(N)₂ [1 μM] alone, dNTP mix [1 μM ea.] and RNase free water to 17 μl at70° C. for 5 minutes followed by immediate removal to ice. Thepolymerase reaction was initiated by addition of 2 μl of 10×MMLV bufferto a final concentration of 75 mM KCL, 50 mM Tris-HCl, 3 mM MgCl₂, 10 mMdithiothreitol, pH 8.3) and 1 μl (200 units) MMLV reverse transcriptase(NEB). Reactions were mixed, and incubated for 1 hour at 42° C. Enzymeactivity was halted by heat inactivation for 5 minutes at 95° C.

Aliquots of the WTA library synthesis reactions corresponding to 10 ngof input RNA (or in the case of the 10 ng sample, the entire reactionmixture) were further amplified by real-time PCR. The PCR reactionmixture contained: 1× Titanium Taq reaction buffer (Clontech), 200 nMeach dNTP, 100,000× dilutions of fluorescein and SyberGreen I (MolecularProbes) 1 μM K_(U) primer (Table III primer 16), 5 units of Titanium Taqpolymerase (Clontech) and volumes representing 10 ng equivalents of theinput polyA+ RNA from the library synthesis reactions in a final volumeof 754 Reactions were carried out for 17 cycles (94° C. for 20 sec and65° C. for 2 min) in real-time PCR I-Cycler™ (Bio-Rad). The effects ofinput template and subsequent reaction volumes transferred into the PCRamplification are seen in FIG. 36. The entire 10 ng library synthesisproduct shows delayed real-time PCR kinetics relative to 10 ng takenfrom the 100 ng library synthesis reaction. The modest effect of theamount of RNA in the library preparation step on the amplificationprofile (only a single cycle shift) suggests only minor differences intemplate availability for these RNA amounts.

One specific application of whole transcriptome amplification is toenable micro-array expression analysis from small amounts of RNA.Traditional RNA amplification methods employ priming of polyA tailspresent within the mRNA pool of transcripts. As a result, themicro-array studies to date have been biased toward the 3′ end of mRNAs.To increase compatibility of the present invention with the existingmicro-array target bias, the K(T)₂₀ primer was employed. To demonstratethe effect of this added priming, the amplifications were tested in thepresence and absence of each primer. FIG. 37 shows a two cycle shift inthe absence of K(T)₂₀ when 10 ng polyA+ RNA serves as template for thelibrary synthesis step, and a six cycle shift in the absence of K(N2).The combined effect of these primers facilitates even priming across themRNA molecules and exhibits a more uniform representation of the inputRNA across the entire message.

Agarose gel electrophoretic analysis of the resulting amplified libraryproducts supports the observed real-time improvements with higher inputtemplate and polyA tail specific priming. FIG. 38 shows the molecularweight range of products amplified from each of these libraries with thevarious primer conditions. The combination of priming both at the polyAtail and at random internal sites yields a more robust amplificationover a larger product size range. The absence of K(T)₂₀ priming has muchless of an effect on performance than does the absence of the K(N)₂primer, which essentially eliminates products competent foramplification by failing to generate the second universal priming siteon each amplicon. 100 ng input template libraries exhibit a broader sizedistribution of amplimers suggestive of less frequent priming or simplya greater starting quantity of larger RNA molecules.

Representation of specific mRNA molecules was evaluated by real-time PCRanalysis for 11 specific human STS markers residing in known genesrepresented in the RNA sample at various levels of expression (Table IV,STS markers: 20, 31, 47, 51, 86, 103, 106, 110, 119, 134, 140). Thematerial amplified by PCR with universal K_(U) primer was purified withQiaquick filters (Qiagen), and 10 ng aliquots were analyzed in real-timePCR. Reactions were carried out for 45 cycles at 94° C. for 15 sec and68° C. for 1 min on I-Cycler (Bio-Rad), in a 25 μl volume. Standardscorresponding to 10, 1, and 0.2 ng of fragmented genomic DNA were usedfor each STS. Quantitation was by standard curve fit for each STS. FIG.39 demonstrates the representation of these STS sites. Each of thechosen STS sites was represented for each condition with noticeableimprovement observed when the K(N)₂ and K(T)₂₀ primers are combined andsomewhat improved average performance for the 100 ng input libraries.

Another unique feature of the invention relates to WTA libraryrepresentation across a particular mRNA locus. One can expect that thecombined terminal and semi-random internal priming generates ampliconsacross the entire RNA molecule population without bias toward the 3′end. To prove this statement three large transcripts were examined usingSTS primer pairs at varying distances from the 3′ end (Table IV STS 42,42a, 42b, 85, 85a, 85b, 119, 119a, 119b). FIG. 40 illustrates thereal-time PCR analysis of WTA amplification for these loci. The resultsindicate representation at all sites with improvement in 3′representation attributed to the inclusion of the K(T20) primer.Relative differences in specific site amplifications are attributed tovariable priming and efficiency of amplification of specific sequences.These results indicate relatively uniform library representation atdifferent distances from the 3′ end for three randomly chosen largetranscripts. Representation is consistent between libraries made from abroad range of RNA input template (100 ng-10 ng). The lower level ofamplification observed at 1795 bp from the 3′ end of STS 42a compared toits neighboring more proximal and more distal sequences (42 and 42b,Table IV) suggests that WTA amplification of specific regions may belargely dependent on the nucleotide sequences surrounding the specificsite of interest. Reproducibility of amplification of specific markersbetween libraries suggests the ability to directly compare expressionlevels of a particular site between two samples (i.e. cancer vs. normaltissue).

Example 20. Whole Transcriptome Amplification: Titration of InputTemplate and MgCl₂ Concentration

WTA amplification of RNA from systematic sampling of tissues such asbiopsy tissues and laser capture micro-dissection, or where sample islimiting as in the case of rare collections from unique cohorts,dictates the need for robust amplification from low input templateamounts. To evaluate the tolerated range of input template and optimalMgCl₂ concentration, total RNA from normal pooled prostate (CPP,Clontech) was examined from 0.25 ng to 10 ng at 3 mM and 10 mM MgCl₂.Annealing was facilitated by briefly heating the mixture of 10 ng, 1 ng,0.5 ng, or 0.25 ng CPP total RNA (Clontech), primers K(N)₂ [1 μM] (TableIII primer 14) and K(T20) [200 nM] (Table III; primer19), dNTP mix [1 μMea.] and RNase free water to 17 μl at 70° C. for 5 minutes followed byimmediate removal to ice. The library synthesis reaction was initiatedby addition of 2 μl of 10×MMLV buffer to a final concentration of 75 mMKCL, 50 mM Tris-HCl, 3 mM or 10 mM MgCl₂, 10 mM dithiothreitol, pH 8.3)and 1 μl (200 units) MMLV reverse transcriptase (NEB) or 1 μl (50 units)MMLV reverse transcriptase (Epicentre). Reactions were mixed, andincubated for 1 hour at 42° C. Enzyme activity was halted by heatinactivation for 5 minutes at 95° C.

The library synthesis reactions were amplified by real-time PCR in areaction mixture that contained: 1× Titanium Taq reaction buffer(Clontech), 200 nM each dNTP, 100,000× dilutions of fluorescein andSyberGreen I (Molecular Probes) 1 μM K_(U) primer (Table III primer 16),5 units of Titanium Taq polymerase (Clontech) and 50% of the librarysynthesis reaction (12.5 μl) representing 5 ng, 0.5 ng, 0.25 ng and0.125 ng of starting template in a final volume of 75 μl. Reactions werecarried out for 17-33 cycles (94° C. for 20 sec and 65° C. for 2 min) inreal-time PCR I-Cycler™ (Bio-Rad). FIG. 41 shows the real-timeamplification profiles with the expected template dependent titration.Doubling of the template results in the expected two fold increase seenas a one cycle shift, while the 10 fold increase from 0.5 ng to 5 nggave slightly more than the expected 10 fold (3.4 cycle) shift. Astriking difference in performance is observed with the two bufferenzyme combinations.

To evaluate the variation in representation across the input templateconcentration and buffer conditions, samples from 10 ng and 0.25 nginput template amounts were evaluated by STS analysis. Representation ofspecific mRNA molecules was evaluated by real-time PCR analysis for 11specific human STS markers residing in known genes represented in theRNA sample at various levels of expression (Table IV, STS markers: 20,31, 47, 51, 86, 103, 106, 110, 119, 134, 140). The material amplified byPCR with universal K_(U) primer was purified with Qiaquick filters(Qiagen), and 10 ng aliquots were analyzed in real-time PCR. Reactionswere carried out for 45 cycles at 94° C. for 15 sec and 68° C. for 1 minon I-Cycler (Bio-Rad), in a 25 μl volume. Standards corresponding to 10,1, and 0.2 ng of fragmented genomic DNA were used for each STS.Quantitation was by standard curve fit for each STS. FIG. 42 shows therelative quantities of each of genes assayed. Reducing the input to 0.25ng under low (3 mM, NEB) MgCl₂ conditions reduces the representation ofrare messages below confidence levels. Representation is markedlyincreased with the increased (10 mM, Epicentre) MgCl₂ conditions aspredicted by the real-time amplification kinetics.

To further examine the difference between the buffer systems, atitration of MgCl₂ concentration was examined. Total RNA from normalpooled prostate (CPP, Clontech) 10 ng was amplified over a 3-12 mM rangeof MgCl₂. Annealing was facilitated by briefly heating the mixture of 10ng CPP total RNA (Clontech), primers K(N)₂ [1 μM] (Table III, primer 14)and K(T)₂₀ [200 nM] (Table III, primer19), dNTP mix [1 μM ea.] and RNasefree water to 17 μl at 70° C. for 5 minutes followed by immediateremoval to ice. The library synthesis reaction was initiated by additionof 2 μl of 10×MMLV buffer to a final concentration of 75 mM KCL, 50 mMTris-HCl, 3 mM or supplemented in 1 mM increments to 12 mM MgCl₂, 10 mMdithiothreitol, pH 8.3) and 411 (50 units) MMLV reverse transcriptase(Epicentre). Reactions were mixed, and incubated for 1 hour at 42° C.Enzyme activity was halted by heat inactivation for 5 minutes at 95° C.The library synthesis reactions were further amplified by real-time PCRin a reaction mixture that contained: 1× Titanium Taq reaction buffer(Clontech), 200 nM each dNTP, 100,000× dilutions of fluorescein andSyberGreen I (Molecular Probes) 1 μM K_(U) primer (Table III, primer16), 5 units of Titanium Taq polymerase (Clontech) and 50% of eachlibrary synthesis reaction (10 μl) representing 5 ng of startingtemplate in a final volume of 75 μl. Reactions were carried out for 19cycles (94° C. for 20 sec and 65° C. for 2 min) in real-time PCRI-Cycler™ (Bio-Rad). FIG. 43 shows real-time PCR curves detailing theeffect of MgCl₂ on WTA library generation. Conditions at or above 6 mMto about 12 mM MgCl₂ during library preparation step yield optimalkinetics. MgCl₂ is known to affect base pairing which can manifestitself at the level of primer binding as well as strand displacement inthe WTA application of the invention. A skilled artisan could determineoptimal concentrations for specific applications of the invention,including parameters such as template size and complexity, for example.

Example 21. Preferential Amplification of Single Stranded Nucleic AcidTemplates Using WTA Methods

In applications where residual DNA may be present in a clinical sample,or where total nucleic acids are isolated, the ability to selectivelyamplify DNA or RNA from the same sample can be beneficial. In thisexample, the WTA protocol is applied to samples of total RNA or genomicDNA with and without fragmentation and denaturation.

To evaluate WTA library formation from DNA and RNA input templates 10 ngsamples of genomic DNA (Coriell CEPH genomic DNA (#7057) or total RNA(Clontech, CPP) were diluted to a final volume of 6.5 μl in water.Fragmentation and denaturation were performed by heating to 95° C. for 4minutes, snap cooling to ice (4° C.), addition of 1.5 μl of 10×MMLVbuffer (Epicentre) to a final concentration of 75 mM KCL, 50 mMTris-HCl, 10 mM MgCl₂, 10 mM dithiothreitol, pH 8.3), primers K(N)₂ [1μM] (Table III primer 14) and K(T)₂₀ [200 nM] (Table III, primer19),dNTP mix [1 μM ea.] and RNase free water to 14 followed by a brief 2minute heating to 95° C. and cooling to ice to anneal primers. Samplesnot fragmented or denatured received standard 70° C. treatment for 5minutes, followed by snap cooling to ice (4° C.) addition of 1.5 μl of10×MMLV buffer (Epicentre) to a final concentration of 75 mM KCL, 50 mMTris-HCl, 10 mM MgCl₂, 10 mM dithiothreitol, pH 8.3), primers K(N)₂ [1μM] (Table III primer 14) and K(T)₂₀ [200 nM] (Table III, primer19),dNTP mix [1 μM ea.] and RNase free water to 14 The polymerase reactionwas initiated by addition of 1 μl (50 units) MMLV reverse transcriptase(Epicentre). Reactions were mixed, and incubated for 15 minutes at 23°C. followed by 1 hour at 42° C. Enzyme activity was halted by heatinactivation for 5 minutes at 95° C.

The library reactions were amplified by real-time PCR in a reactionmixture that contained: 1× Titanium Taq reaction buffer (Clontech), 200nM each dNTP, 100,000× dilutions of fluorescein and SyberGreen I(Molecular Probes) 1 μM K_(U) primer (Table III primer 16), 5 units ofTitanium Taq polymerase (Clontech) and 100% of the library reaction (15μl) representing the entire 10 ng of starting template in a final volumeof 75 μl. Reactions were carried out for 13-17 cycles (94° C. for 20 secand 65° C. for 2 min) in real-time PCR I-Cycler™ (Bio-Rad). FIG. 44Ashows the real-time amplification profiles from each template. Librariesamplified from DNA after fragmentation and denaturation show profilessimilar to WGA embodiments of the invention. As claimed, MMLV polymeraseactivity can efficiently substitute for other polymerases in WGA librarysynthesis. In the absence of fragmentation and denaturation, DNA isseverely inhibited, showing an approximately 6 cycle delay inamplification, or roughly 1% of template participating in the reaction.RNA templates only display a minor effect of fragmentation anddenaturation conditions compared to direct annealing and extension.Differences in the molecular weight of products amplified in each ofthese reactions and the control reactions without template are shown inFIG. 44B. Each reaction was allowed to proceed to plateau and evaluatedby agarose gel electrophoresis. The distribution of library fragmentsfrom DNA template is consistent with that observed for WGA products.Thermal treatment of RNA shifts the size distribution of libraryfragments by 50 to 100 base pairs shorter, demonstrating the ability totailor amplicon size. No template controls failed to generate ampliconsabove 200 bp after 28 cycles of amplification.

The ability to distinguish between DNA and RNA templates on the basis offragmentation and denaturation demonstrate controlled differentialaccess of the template. Residual traces of DNA in RNA preparations willamplify with approximately 1% efficiency with respect to the RNAtemplate under non-denaturing conditions. Although not specificallydemonstrated here, as known in the art, Klenow exo− fails to utilize RNAas a template, thereby providing a method to selectively amplify eachnucleic acid population from a complex mixture.

Example 22. Total Nucleic Acid Differential Amplification Platform forSynthesis of DNA and RNA Libraries from Limited Archived or ClinicalSamples

In some genetic profiling studies, both the genomic (DNA) and theexpression (RNA) information are required to provide a complete analysisof the tissue or cells evaluated. Only when alterations in genesequence, copy number, and the effective expression of transcribedsequences are taken together can a complete analysis of the sample beachieved. In many cases, a clinical isolate or archival sample islimited and may only be sufficient for one isolation scheme.Amplification of genomic and expression libraries may be streamlinedthrough a total amplification platform using the present invention.

FIG. 45 illustrates selective amplification of DNA and RNA from a totalnucleic acid isolate using self-inert degenerate primers in combinationwith Klenow Exo− fragment of DNA polymerase I and heat-denatured nucleicacid (WGA) or MMLV reverse transcriptase and non-denatured nucleic acid(WTA). A device is diagrammed for the segregation of DNA and RNA byselective amplification from a total nucleic acid preparation. Theinvention applied in this format, or applied in a microfluidic platform,for example, uses selective amplification rather than selectivedegradation or selective isolation of DNA and RNA, eliminating problemssuch as sample loss associated with preparation of nucleic acids fromlimited samples.

Example 23. Application of Homopolymeric G/C Tagged WGA Libraries forTargeted DNA Amplification

Targeted amplification may be applied to genomes for which limitedsequence information is available or where rearrangement or sequenceflanking a known region is in question. For example, transgenicconstructs are routinely generated by random integration events. Todetermine the integration site, directed sequencing or primer walkingfrom sequences known to exist in the insert may be applied. Theinvention described herein can be used in a directed amplification modeusing a primer specific to a known region and a universal primer. Theuniversal primer is potentiated in its ability to amplify the entirelibrary, thereby substantially favoring amplification of product betweenthe specific primer and the universal sequence, and substantiallyinhibiting the amplification of the whole genome library.

Conversion of WGA libraries for targeted applications involvesincorporation of homo-polymeric terminal tags. Amplification oflibraries with C-tailed universal primers exhibit a dependence on thelength of the 5′ poly-C extension component of the primer. WGA librariesprepared by the methods described in the invention can be converted fortargeted amplification by PCR re-amplification using poly-C extensionprimers. FIG. 46A shows potentiated amplification with increasing lengthof poly-C in real-time PCR. The reduced slope of the curves for C₁₅U andC₂₀U show delayed kinetics and suggest reduced template availability orsuppression of priming efficiency.

To demonstrate the suppression of library amplification imposed bypoly-C tagging, libraries were purified using Qiaquick PCR purificationcolumn (Qiagen) and subjected to PCR amplification with poly-C primerscorresponding to the length of their respective tag. FIG. 46B showsreal-time PCR results that reflect the suppression of whole genomeamplification. Only the short C₁₀ tagged libraries retain a modestamplification capacity, while C₁₅ and C₂₀ tags remain completelysuppressed after 40 cycles of PCR.

Example 24. Application of Homopolymeric G/C Tagged WGA Libraries forMultiplexed Targeted DNA Amplification

Application of G/C tagged libraries for targeted amplification uses asingle specific primer to amplify a plurality of library amplimers. Thecomplexity of the target library dictates the relative level ofenrichment for each specific primer. In low complexity bacterial genomesa single round of selection is sufficient to amplify an essentially pureproduct for sequencing or cloning purposes, however in high complexitygenomes a secondary, internally “nested”, targeting event may benecessary to achieve the highest level of purity.

Using a human WGA library with C₁₀ tagged termini incorporated byre-amplification with C-tailed universal U primers, specific sites weretargeted and the relative enrichment evaluated in real-time PCR. FIG.47A shows the chromatograms from real-time PCR amplification forsequential primary 1° and secondary 2° targeting primers in combinationwith the universal tag specific primer C₁₀, or C₁₀ alone. The enrichmentfor this particular targeted amplicon achieved in the primaryamplification is approximately 10,000 fold. Secondary amplification witha nested primer enriches to near purity with an additional two orders ofmagnitude for a total enrichment of 1,000,000 times the startingtemplate. It is understood to those familiar with the art thatenrichment levels may vary with primer specificity, while primers ofhigh specificity applied in sequential targeted amplification reactionsgenerally combine to enrich products to near purity.

To apply targeted amplification in a multiplexed format, specific primerconcentrations were reduced 5 fold (from 200 nM to 40 nM) withoutsignificant loss of enrichment of individual sites (FIG. 47B). Thisprimer concentration reduction allows for the combination of 45 specificprimers and universal C₁₀ primer to maintain total primer concentrationswithin reaction tolerances [2 μM].

To evaluate the utility of multiplex-targeted amplification, a set ofprimers were designed adjacent to STS sites (Table IV) using OligoVersion 6.53 primer analysis software (Molecular Biology Insights, Inc.:Cascade Colo.). Primers were 18-25 bases long, having high internalstability, low 3′-end stability, and melting temperatures of 57-62° C.(at 50 mM salt and 2 mM MgCl₂). Primers were designed to meet allstandard criteria, such as low primer-dimer and hairpin formation, andare filtered against a human genomic database 6-mer frequency table.Primary multiplexed targeted amplification of G/C tagged WGA librarieswas performed using 10-50 ng of tagged WGA library, 10-40 nM each of 45specific primers (Table VI), 200 nM C₁₀ primer, dNTP mix, 1×PCR bufferand 1× Titanium Taq polymerase (Clontech), FCD (1:100,000) and SGI(1:100,000) dyes (Molecular Probes) added for real-time PCR detectionusing the I-Cycler (Bio-Rad). Amplification is carried out by heatingthe samples to 95° C. for 3′30″, followed by 18-24 cycles of 94° C. 20″,68° C. 2′. The cycle number to reaction plateau is dependent on theabsolute template and primer concentrations. The amplified material waspurified by Qiaquick spin column (Qiagen), and quantifiedspectrophotometrically.

The enrichment of each site was evaluated using real-time PCR.Quantitative Real-Time PCR was performed using an I-Cycler Real-TimeDetection System (Bio-Rad), as per the manufacturer's directions.Briefly, 25 μl reactions were amplified for 40 cycles at 94° C. for 15sec and 68° C. for 1 min. Standards corresponding to 10, 1, and 0.2 ngof fragmented DNA were used for each STS, quantities were calculated bystandard curve fit for each STS (I-Cycler software, Bio-Rad) and wereplotted as distributions. FIG. 48A shows the relative fold amplificationfor each targeted site. Primary amplification of sites 1 and 29 failedto amplify in multiplex reactions and displayed delayed kinetics insinglet reactions (not shown). A distribution plot of the same datashows an average enrichment of 3000 fold (FIG. 48B). Differences inenrichment level such as highly over-amplified sites are likely to arisefrom false priming elsewhere on the template. Such variation iscompensated with the use of nested amplification of the enrichedtemplate.

Secondary targeted amplifications were performed using primary targetingproducts as template and secondary nested primers (Table VI) incombination with the universal C₁₀ primer. Reactant concentrations andamplification parameters were identical to primary amplifications above.Multiplexed secondary amplifications were purified by Qiaquick spincolumn (Qiagen) and quantified by spectrophotometer. Enrichment ofspecific sites was evaluated in real-time PCR using an I-CyclerReal-Time Detection System (Bio-Rad), as per the manufacturer'sdirections. Briefly, 25 μl reactions were amplified for 40 cycles at 94°C. for 15 sec and 68° C. for 1 min. Standards corresponding to 10, 1,and 0.2 ng of fragmented DNA were used for each STS, quantities werecalculated by standard curve fit for each STS (I-Cycler software,Bio-Rad) and were plotted as distributions. FIG. 49A shows the relativeabundance of each site after nested amplification and FIG. 49B plots thedata in terms of frequency.

Targeted amplification applied in this format reduces the primercomplexity required for multiplexed PCR. The resulting pool of amplimerscan be evaluated on sequencing or genotyping platforms.

Example 25. Non-Redundant Genomic Sequencing of Unculturable or LimitedSpecies Facilitated by Whole Genome and Targeted Amplification

Whole genome and targeted amplification provide a unique opportunity forsequencing genomes of microorganisms which are difficult to grow or forspecies that are already extinct. The diagram illustrating such ahypothetical DNA sequencing project is shown on the FIG. 50. First,limited amounts of DNA for the organism of interest (FIG. 50A) areconverted into WGA library using any method described above or asdescribed in U.S. Patent Application 60/453,071, filed Mar. 7, 2003, andthe U.S. Nonprovisional Patent Application claiming priority to same andfiled concomitantly herewith, and amplified (FIG. 50B). Second, afraction of amplified WGA DNA is cloned in a bacterial vector (FIG. 50C)while another fraction of amplified WGA DNA is converted into C-taggedWGA library (FIG. 50D). Third, the cloned DNA is sequenced with minimalredundancy (FIG. 50E) to generate enough sequence information toinitiate targeted sequencing and “walking” (FIG. 50F) that shouldultimately result in sequencing of all gaps remaining afternon-redundant sequencing and finishing the sequencing project (FIG.50G). The outlined strategy can be used not only for sequencing oflimited species but also in any large DNA sequencing projects byreplacing the costly and tedious highly redundant “shotgun” method.

TABLE VI Targeted Amplification Primers Primary Secondary STS 1PGCATATCCATATCTCCCGAAT STS 1S TAAGCAGCAAGGTCTGGG (SEQ ID NO: 30)(SEQ ID NO: 75) STS 2P CAGAGCACTCCAGACCATACG STS 2SGTGATTGAACAATTTGGACCCAC (SEQ ID NO: 31) (SEQ ID NO: 76) STS 3PCTTCGTTATGACCCCTGCTCC STS 3S ATGGCAACATTCCACCTAGTAGC (SEQ ID NO: 32)(SEQ ID NO: 77) STS 4P TCCCAAGATGAATGGTAAGACG STS 4SCTCCGTCATGATAAGATGCAGT (SEQ ID NO: 33) (SEQ ID NO: 78) STS 5PTCCAATCTCATCGGTTTACTG STS 5S ACTGTTTGGGGTGTGAAAGGAC (SEQ ID NO: 34)(SEQ ID NO: 79) STS 8P TCCAGAGCCCAGTAAACAACA STS 8S ACTAACAACGCCCTTTGCTC(SEQ ID NO: 35) (SEQ ID NO: 80) STS 10P  TTACTTCAGCCCACATGCTTC STS 10STCAGCACTCCGTATCTTCATTTG (SEQ ID NO: 36) (SEQ ID NO: 81) STS 12PTTCCGACATAGCGACTTTGTAG STS 12S TAAACCGCTAAAACGATAGCAGC (SEQ ID NO: 37)(SEQ ID NO: 82) STS 14P AAGGATCAGAGATACCCCACGG STS 14STCATGGTATTAGGGAAGTGGGAG (SEQ ID NO: 38) (SEQ ID NO: 83) STS 16PTCCAAGAACCAACTAAGTCCAGA STS 16S GGGAATGAAAAGAAAAGGCATTC (SEQ ID NO: 39)(SEQ ID NO: 84) STS 22P CTAAGGGCAAACATAGGGATCAA STS 22STCTTTCCCTCTACAACCCTCTAACC (SEQ ID NO: 40) (SEQ ID NO: 85) STS 26PCAACCTTTGAAGCCACTTTGAC STS 26S CAGTACATGGGTCTTATGAGTAC (SEQ ID NO: 41)(SEQ ID NO: 86) STS 29P GCCTCCGTCATTGGTATTTTCT STS 29SAATCGAGAACGCACAGAGCAGA (SEQ ID NO: 42) (SEQ ID NO: 87) STS 30PTGGCAACACGGTGCTGACCTG STS 30S GTCTGGGGAGTAAATGCAACATC (SEQ ID NO: 43)(SEQ ID NO: 88) STS 31P ATCATGGGTTTGGCAGTAAAGC STS 31STTCTTGATGACCCTGCACAA (SEQ ID NO: 44) (SEQ ID NO: 89) STS 35PAGAACCAGCAAACCCAGTCCC STS 35S CAGCAGAAGCACTACCAAAGACA (SEQ ID NO: 45)(SEQ ID NO: 90) STS 36P GAAAGGGTGGATGGATTGAAA STS 36STTCACCTAGATGGAATAGCCACC (SEQ ID NO: 46) (SEQ ID NO: 91) STS 38PTCAGATTTCCTGGCTCCGCTT STS 38S GCAAGATTTTTGCTTGGCTCTAT (SEQ ID NO: 47)(SEQ ID NO: 92) STS 41P CCTTCTGCTTCCCTGTGACCT STS 41SGAATTTTGGTTTCTTGCTTTGG (SEQ ID NO: 48) (SEQ ID NO: 93) STS 42PTGAACCCCACGAGGTGACAGT STS 42S GTCAGAAGACTGAAAACGAAGCC (SEQ ID NO: 49)(SEQ ID NO: 94) STS 43P GACATTACCAGCCCCTCACCTA STS 43SCATCTCTTGATCATCCCAGCTCT (SEQ ID NO: 50) (SEQ ID NO: 95) STS 44PTCCTTGACAGTTCCATTCACCA STS 44S CACCATTGGTTGATAGCAAGGTT (SEQ ID NO: 51)(SEQ ID NO: 96) STS 46P TTTGCAGGTAGCTCTAGGTCA STS 46STAAACATAGCACCAAGGGGC (SEQ ID NO: 52) (SEQ ID NO: 97) STS 47PGCGGACAGAGAGTAACCTCGGA STS 47S TCATGTGTGGGTCACTAAGGATG (SEQ ID NO: 53)(SEQ ID NO: 98) STS 49P CCCAGAAACCCTGAGACCCTC STS 49SCGTCTCTCCCAGCTAGGATG (SEQ ID NO: 54) (SEQ ID NO: 99) STS 52PTGTGCCACAAGTTAAGATGCT STS 52S CTTTTTCACAGAACTGGTGTCAGG (SEQ ID NO: 55)(SEQ ID NO: 100) STS 54P TGCTGTATCGTGCCTGCTCAAT STS 54SACCCAGCTTTCAGTGAAGGA (SEQ ID NO: 56) (SEQ ID NO: 101) STS 60PTGCCCCACTCCCCAACATTCT STS 60S AATCAAAAGGCCAACAGTGG (SEQ ID NO: 57)(SEQ ID NO: 102) STS 62P AACAGAGCCTCAGGGACCAGT STS 62SACTGGCTGAGGGAGCATG (SEQ ID NO: 58) (SEQ ID NO: 103) STS 70PGGGCTTTGTCTGTGGTTGGTA STS 70S TAAATGTAACCCCCTTGAGCC (SEQ ID NO: 59)(SEQ ID NO: 104) STS 72P TGGGCTGGCTGAGGTCAAGAT STS 72STATTGACCACATGACCCCCT (SEQ ID NO: 60) (SEQ ID NO: 105) STS 74PTTTTGCTCCGCTGACATTTGG STS 74S TTGGGTGATGTCTTCACATGG (SEQ ID NO: 61)(SEQ ID NO: 106) STS 77P TGCTCCTGTCCCTTCCACTTC STS 77S GCTCAATAAAAATAGTACGCCC (SEQ ID NO: 62) (SEQ ID NO: 107) STS 79PCCTTATTCCCAGCAGCAGTATTC STS 79S TTCTCCCAGCTTTGAGACGT (SEQ ID NO: 63)(SEQ ID NO: 108) STS 82P TGGGAAGGGAAAGAGGGTACT STS 82STTTGTTACTTGCTACCCTGAG (SEQ ID NO: 64) (SEQ ID NO: 109) STS 83PTTGCTGTAGATGGGCTTTCGT STS 83S GAAGATGAAGTGAACTCCTATCC (SEQ ID NO: 65)(SEQ ID NO: 110) STS 84P TCTGCTGGGTTGATGATTTGG STS 84SGAAGCCTTGATAACGAGAGTGG (SEQ ID NO: 66) (SEQ ID NO: 111) STS 85PGGCACAAGCAAAAGGGTGTCT STS 85S ATGTTTCTCTGGCCCCAAG (SEQ ID NO: 67)(SEQ ID NO: 112) STS 86P CCAGCAATCAGGAAAGCACAA STS 86S TGGCTGCCCTTCAATAC(SEQ ID NO: 68) (SEQ ID NO: 113) STS 89P CACCTGTCTTGTTGGCATCACC STS 89STTGGGAAATGTCAGTGACCA (SEQ ID NO: 69) (SEQ ID NO: 114) STS 92PTTGTTTTGCCTCACCAGTCATTT STS 92S TGTGGTTAGGATAGCACAAGCATT (SEQ ID NO: 70)(SEQ ID NO: 115) STS 96P TCAGCAAACCCAAAGATGTTA STS 96STGCAATTTGAAGGTACGAGTAG (SEQ ID NO: 71) (SEQ ID NO: 116) STS 99PTTAGTCCTTTGGGCAGCACGA STS 99S TGTTAACAATTTGCATAACAAAAGC (SEQ ID NO: 72)(SEQ ID NO: 117) STS103P TGTCTCTGCTTCTGAAACGGG STS1035GCATTTTCTGTCCCACAAGATATG (SEQ ID NO: 73) (SEQ ID NO: 118) STS113PACTGCCAGGGTCATTGACTT STS1135 ATTGCTGTCACAGCACCTTG (SEQ ID NO: 74)(SEQ ID NO: 119) *P- denotes primary targeted amplification primer *S-denotes secondary targeted amplification primer

Example 26. Universality of the Novel Nucleic Amplification Method andits Compatibility with Different Sources of DNA and RNA and DifferentMethods of Analysis of the Amplified Material

The diagram presented on FIG. 51 illustrates the diversity of DNA andRNA samples that are compatible with the proposed method ofamplification of nucleic acid, universality of the amplificationtechnique, and the diversity of possible applications.

Nucleic acid sources include but not limited to all animals (includinghumans), plants, fungi, culturable and non-culturable bacteria andviruses, and extinct species found in amber and stones. They can beisolated from any fresh, frozen, or paraffin embedded formalin fixedtissue, body fluids, forensic sample, cell culture, single cell, singlechromosome, etc.

The library preparation step can use total nucleic acid as a template(the protocol shown in central part of the diagram, arrow A), and resultin the amplification of both DNA and RNA, or use purified DNA, andresult in the amplification of the whole genome (the protocol shown inleft part of the diagram, arrow B), or use purified RNA, and result inthe amplification of the whole transcriptome (the protocol shown inright part of the diagram, arrow C), or use total nucleic acid and acorresponding selection method, and result in the amplification of thewhole genome (the protocol shown in left part of the diagram, arrow D),or whole transcriptome (the protocol shown in right part of the diagram,arrow E).

Library prepared and amplified from total nucleic acid, DNA, or RNA canbe modified to incorporate polyC regions at the 5′ end of the universalconstant sequence (arrows F and G). C-tailed libraries can be used fortargeted amplification and analysis of specific genomic regions or RNAtranscripts.

Library prepared and amplified from total nucleic acid, DNA, or RNA canbe modified to incorporate other tags (see FIG. 19-25) and used for IDidentification, immobilization on a solid support or a micro-array, ormultiple usage (not shown in FIG. 51).

Applications of the proposed nucleic acid amplification technologyinclude but not limited to genotyping of small DNA/RNA samples, geneexpression analysis, sequencing of un-culturable or extinct organisms,molecular diagnostics of different diseases, prenatal diagnostics,viral/bacterial diagnostics, forensics, etc.

Example 27. Amplification of Genomic DNA from Single Cells Using aMesophilic DNA Polymerase Followed by Universal-Primer PCR with aThermostable DNA Polymerase, and Analysis of Locus Representation byReal-Time PCR

This example describes the synthesis of libraries from single cells withKlenow Exo-followed by amplification with Taq DNA polymerase andanalysis of their locus representation by real-time PCR.

Immortalized human prostate epithelial RWPE cells were trypsinized,washed three times with PBS, and single cells were collected by FlowCytometry in 5 ul of TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA).Control samples containing either 5 cells or just TE buffer were alsoincluded in the analysis to assess the locus representation of more thanone genome equivalent and the amplification background respectively.Cells were immediately frozen on dry ice after collection and stored at80° C. prior to use.

Wells containing sorted cells were thawed on ice and DNA was extractedby addition of 5 ul of freshly prepared 2× cell lysis buffer comprising:0.015% SDS, 40 mM NaCl, 20 mM Tris-HCl pH 7.5, 0.2 mM EDTA, 0.24 mg/mLProteinase K and incubated for 1 hour at 50° C., followed by 4 min at99° C. Samples were briefly centrifuged and placed on ice. Four μL oflibrary synthesis buffer comprising 37.5 mM Tris-HCl pH 7.5, 18.75 mMMgCl₂, 28.125 mM DTT, 0.75 mM each dNTP, 0.05 mg/mL E. coli SSB, andoligonucleotide 3 (Table VII, SEQ ID NO:128) were added to each well andthe samples were heated at 95° C. for 2 min and cooled on ice.

Library synthesis was initiated by addition of 1 μl of Klenow exo at 5Units/uL. Samples were incubated in a thermal cycler as follows: 16° C.for 20 minutes, 24° C. for 20 minutes, 37° C. for 20 minutes, 75° C. for5 minutes. Libraries were further amplified to saturation by real-timePCR on BioRad i-Cycler by addition of 60 ul of library amplificationbuffer comprising: 1.25× Titanium Taq buffer (BD-Clontech), 0.5 mM eachdNTP, 7 mM MgCl₂, 2.5 uM oligonucleotide 4 (Table VII, SEQ ID NO:129),0.6× Titanium Taq DNA polymerase (BD-Clontech), and 10000:1 dilutions offluorescein calibration dye and SybrGreen I (Life Technologies). Afterinitial denaturation at 95° C. for 3 min samples were incubated for 29cycles at 94° C. for 30 sec and 68° C. for 2 min. Library DNA waspurified using MultiScreen HTS PCR kit (Millipore Cat #MSNU03050)following manufacturer's instructions, quantified using absorbance at260 nm, and 50 ng aliquots were used in locus-specific PCR forrepresentation analysis.

Results show exemplary amplification of 4 individual libraries fromsorted single cells, one library of sorted 5 cells, and duplicate “nocells” controls. Locus representation of libraries from sorted cells wasanalyzed by real-time PCR using a panel of 40 human genomic STS andpromoter assays (Table VIII). The PCR reaction mixture comprised: 1×Titanium Taq reaction buffer (Clontech), 200 uM each dNTP, 0.2 uM ofeach forward and reverse primer, 0.5 ul of Titanium Taq polymerase(Clontech), 50 ng library DNA, and 5000:1 dilutions of fluorescein andSybrGreen I (Life Technologies) in a final volume of 25 ul. In the caseof analyzing promoter sequences 4% DMSO and 0.5 M betaine were added tothe reaction mixture.

After initial denaturation for 3 min reactions were carried out at 95°C. for 20 sec, 68° C. for 1 min, 75° C. for 30 sec, and 80° C. for 15sec on i-Cycler real-time PCR instrument (BioRad). Statistical analysisof data was performed using Excel (Microsoft).

Example 28. Amplification of Genomic DNA from Single Cells Using aThermostable DNA Polymerase and Analysis of Locus Representation byReal-Time PCR

This example describes the amplification of genomic DNA from singlecells sorted by Flow Cytometry and the analysis of its locusrepresentation by real-time PCR.

Immortalized human prostate epithelial RWPE cells were trypsinized,washed three times with PBS and single cells were collected by FlowCytometry into 5 ul of cell lysis buffer comprising 5 mM Tris-HCl pH8.3, and 0.01% Triton X-100 in deionized nuclease-free water. Controlsamples containing either 5 cells or just lysis buffer (no cells) werealso included in the analysis to assess the locus representation of morethan one genome equivalent and the amplification backgroundrespectively. Cells were immediately frozen on dry ice after collectionand stored at −80° C. prior to use.

Wells containing sorted cells were thawed on ice and DNA was extractedby addition of 4 ul of cell lysis buffer containing 0.2 units ofproteinase enzyme (prepGEM Saliva 500 Kit, VWR Catalog #95044-052) andincubated for 10 min at 75° C. Five ul of library preparation buffercomprising: 3×KAPA 2G Robust buffer B (KAPA Biosystems, Cat #KB 5003),0.6 mM each dNTP, 6 mM MgCl₂, 12% DMSO, 6 uM oligonucleotide 1 (TableVII, SEQ ID NO:25) [or alternatively 15 uM oligonucleotide 5 (Table VII,SEQ ID NO:130)] were added to each well and the samples were heated at95° C. for 4 min.

Library synthesis was initiated by addition of 1 ul of KAPA 2G RobustDNA polymerase (KAPA Biosystems, Cat #KE 5004) at a concentration of 1unit/ul. After initial denaturation for 2 min at 95° C. samples wereincubated for 12 cycles at: 95° C. for 15 sec, 15° C. for 50 sec, 25° C.for 40 sec, 35° C. for 30 sec, 65° C. for 40 sec, and 75° C. for 40 sec.

Libraries were further amplified to saturation by real-time PCR onBioRad Cycler by addition of 60 ul of library amplification buffercomprising: 1.25×KAPA 2G Robust buffer B (KAPA Biosystems, Cat #KB5003), 0.5 mM each dNTP, 3.75 mM MgCl₂, 6.25% DMSO, 2.5 uMoligonucleotide 2 (Table VII, SEQ ID NO:26), 4.5 units of KAPA 2G RobustDNA polymerase (KAPA Biosystems, Cat #KE 5004), and 5000:1 dilutions offluorescein calibration dye and SybrGreen I (Life Technologies).

After initial denaturation at 95° C. for 2 min samples were incubatedfor 13 cycles at 96° C. for 15 sec, 65° C. for 1 min, and 75° C. for 1min. Library DNA was purified using MultiScreen HTS PCR kit (MilliporeCat #MSNU03050), and 50 ng aliquots were used in locus-specific PCR forrepresentation analysis.

Locus representation of libraries from sorted cells was analyzed byreal-time PCR using a panel of 40 human genomic STS and promoter assays(Table VIII). The PCR reaction mixture comprised: 1× Titanium Taqreaction buffer (Clontech), 200 uM each dNTP, 0.2 uM of each forward andreverse primer, 0.5 ul of Titanium Taq polymerase (Clontech), 50 nglibrary DNA, and 5000:1 dilutions of fluorescein and SybrGreen I (LifeTechnologies) in a total volume of 25 ul. In the case of analyzingpromoter sequences 4% DMSO and 0.5 M betaine were also added to thereaction mixture. After initial denaturation for 3 min reactions werecarried out at 95° C. for 20 sec, 68° C. for 1 min, 75° C. for 30 sec,and 80° C. for 15 sec on i-Cycler real-time PCR instrument (BioRad).Statistical analysis of data was performed using Excel (Microsoft).

FIG. 52 shows an exemplary amplification of replicate single-cell andcontrol no-cell whole genome amplification reactions. It demonstratesthe ability of the methods and compositions disclosed herein to amplifyDNA from a single genome with much higher sensitivity and farther awayfrom the non-specific background characteristic of other methodsgenerally used in the field. This should make it possible to apply thedisclosed methods and compositions for analysis of individualchromosomes as well as limited number of bacterial cells and even viralgenomes.

An exemplary amplification of 10 individual libraries from sorted singlecells, duplicate sorted 5 cells, and quadruplicate “no cells” controlsis shown on FIG. 53. It demonstrates that highly consistent andreproducible results are generated by the methods and compositionsdisclosed in the present invention with small sample-to-samplevariation.

FIG. 54 demonstrates the input range and reproducibility of whole genomeDNA amplification by the methods and compositions disclosed herein. FIG.54A shows locus-specific qPCR testing of whole genome amplification fromreplicate samples corresponding to increasing number of cell equivalentinputs in the range of 1-10,000. FIG. 54B shows that after saturatingwhole genome amplification form 1, 10, 100, or 1000 cell equivalents thecopy number of a single locus as analyzed by qPCR gives practically thesame results.

In quantitative genome analysis sample to sample variation represents asignificant problem. FIG. 55 shows cell to cell variation for twoindividual cells in 24 qPCR assays. As seen from the correlation plothighly reproducible representation over multiple loci is achieved by themethods and compositions disclosed in the present invention.

FIG. 56 illustrates the reproducibility of whole genome amplification bythe disclosed methods and compositions in representing 25 individualloci assayed by qPCR across 10 replicate cells. This figure demonstratesthat there is inherent amplification bias but it is highly reproducibleand can be easily corrected for, a feature that can be highlyadvantageous in quantitative genome analysis.

Example 29. Analyzing Amplification Efficiency

Sample amplification efficiencies can be analyzed by performing theamplification reactions with SYBR® Green I in a real-time thermalcycler. During the amplification reaction, double-stranded amplifiedmolecules are bound by the nonsequence-dependent SYBR® Green I dye, andthe accumulation of amplified product is detected as an increase influorescence by the real-time instrument.

Data analysis is performed on raw background-subtracted fluorescence,and the instrument/software should be set to the appropriate mode.

Amplification curves will have a similar appearance for successfullyamplified single-cell WGA products, with an immediate 8-9 cycle upwardsloping phase, followed by a relatively flat “plateau” phase (FIG. 52).

No-cell control amplification curves are delayed (right-shift) by 5-6PCR cycles compared to single-cell amplification curves. A smaller delayof control curves may indicate DNA contamination introduced with thesample or during the WGA process.

Example 30. Protocol

1. Add 5 uL of PicoPlex Pre-Amp Buffer to 9 uL of single-cell lysate orcontrol no-cell lysate.

2. Incubate samples in a thermal cycler as follows:

1 cycle 95 C. 4 min 1 cycle Room Hold Temp

3. Briefly centrifuge samples. 4. Combine the following components andmix well.

Synthesis Enzyme Mix Volume Per 5 samples Pre-Amp Enzyme Dilution Buffer4 uL PicoPlex Pre-Amp Enzyme 1 uL Total Volume 5 uL

5. Add 1 uL of Pre-Amp Enzyme Mix to sample. 6. Incubate samplesaccording to thermal cycler program below:

1 cycle 95 C.  2 min 95 C. 15 sec 15 C. 50 sec 12 cycles 25 C. 40 sec 35C. 30 sec 65 C. 40 sec 75 C. 40 sec 1 cycle  4 C. hold

7. Briefly centrifuge samples and place synthesis reaction products onice. 8. Combine the following Amplification Cocktail components and mixwell.

Amplification Cocktail Volume Per 5 Samples PicoPlex AmplificationBuffer 125 uL PicoPlex Amplification Enzyme  4 uL Nuclease-Free Water171 uL Total Volume 300 uL Note: Sample amplification efficiencies canbe analyzed by adding SYBR Green I dye (Invitrogen, S7563) at 0.125xfinal concentration in the Amplification Cocktail and by performing theamplification in a real-time thermal cycler (see Appendix A). Someinstruments may also require additional reference dyes for SYBR signalnormalization.

9. Mix 60 uL of the freshly prepared Amplification Cocktail with the 15uL synthesis reaction product and mix by pipet. 10. Amplify samplesaccording to thermal cycler program below:

1 cycle 95 C. 2 min 95 C. 15 sec  13 cycles 65 C. 1 min 75 C. 1 minNote: 13 cycles is recommended in certain embodiments based on testingperformed with single cultured cells obtained by flow sorting, dilution,and micromanipulation. Some cell types or lysis conditions may requireadditional cycles (up to 15) to obtain maximal yields.

Example 31. Exemplary Kit Materials and Methods

The methods and compositions disclosed herein amplify DNA directly frommany types of cells. Some of the methods used in the isolation andamplification of DNA from cells are as follows:

Single Cell Collection Methods

Flow sorting, dilution, and micromanipulation are collection methodsthat are compatible with the methods and compositions disclosed herein.Cell staining may negatively affect whole genome amplificationperformance, especially staining methods that include fixing (e.g. withformaldehyde) steps.

Sample Volume

Single cells may be collected and lysed/extracted in a total of about 9μL volume.

Cell Lysis and DNA Extraction Methods

Single-cell PCR lysis/extraction methods (e.g. protease/detergentincubation or alkaline treatment followed by neutralization) arecompatible with the methods and compositions disclosed herein, as longas, for example, monovalent salt concentrations do not exceed 20 mM inthe final 9 μL lysate volume.

Considerable (>5 μL) evaporation may occur, if the incubation is beingperformed in a PCR plate without a very tight seal. Evaporation duringPCR may be minimized by using an appropriate thermal cycler, forexample, the combination of iCycler IQ 96-well PCR plates (Bio-Rad,223-9441) and Axymat silicone sealing mats (Axygen, AM-96-PCR-RD).

Exemplary Kit Components

Component Name 1. PicoPlex Pre-Amp Buffer 2. PicoPlex Pre-Amp Enzyme 3.Pre-Amp Enzyme Dilution Buffer 4. PicoPlex Amplification Buffer 5.PicoPlex Amplification Enzyme 6. Nuclease-Free Water

TABLE VII OLIGONUCLEOTIDE SEQUENCES USED IN SINGLEGENOME LIBRARIES PREPARATION No Sequence 5′-3′ * 1.TGTGTTGGGTGTGTTTGGKKKKKKKKKK (SEQ ID NO: 25) 2. TGTGTTGGGTGTGTTTGG(SEQ ID NO: 26) 3. TGTTGTGGGTTGTGTTGGKKKKKKKKKK (SEQ ID NO: 128) 4.TGTTGTGGGTTGTGTTGG (SEQ ID NO: 129) 5. TGTGTTGGGTGTGTTTGGNKKNKKNKK(SEQ ID NO: 130) * Random bases definitions: K = G, T; N = A, G, C, T

TABLE VIII OLIGONUCLEOTIDE SEQUENCES USED IN LOCUS-SPECIFIC REAL-TIME PCR ASSAYS Assay No *** Sequence 5′-3′ **  1F AGAGGCTTCTGGCAGTTTGC (SEQ ID NO: 131)  1 R CCCAGCCTCTGGAAAATCAG(SEQ ID NO: 132)  2 F CCCTAACATGGAGGTAGGAGC (SEQ ID NO: 133)  2R TCTTCCTGGTGTGAGCCTCT (SEQ ID NO: 134)  3 F GAGAACCGGAGCGTGCTT(SEQ ID NO: 135)  3 R TATTGACCACATGACCCCCT (SEQ ID NO: 136)  4F GCAAAATCCATACCCTTTCTGC (SEQ ID NO: 137)  4 R TCTTTCCCTCTACAACCCTCTAACC(SEQ ID NO: 138)  5 F GCAAAATGCCTTCTTGTGTTTTTC (SEQ ID NO: 139)  5R GCATTTTCTGTCCCACAAGATATG (SEQ ID NO: 140)  6 F ATGTTTCTCTGGCCCCAAG(SEQ ID NO: 141)  6 R TTCTCCATGAGATTGGACTGG (SEQ ID NO: 142) 10F TCATCATGATCAACAGGAAAGA (SEQ ID NO: 143) 10 R CAACCCTGGCCTCAGGAT(SEQ ID NO: 144) 11 F GTGAATATAGTGAGTGACAGATGGC (SEQ ID NO: 145) 11R CTTTATGAAACGGGGCCATA (SEQ ID NO: 146) 12 F CAATGTACAGGTCCTGTTGCC(SEQ ID NO: 147) 12 R AAAACAATGCTTCCAGTGGC (SEQ ID NO: 148) 13F ACAGTCCCATTCTGGCAAAC (SEQ ID NO: 149) 13 R TCACTCCCTCCAACAATTCC(SEQ ID NO: 150) 14 F TTTGTTACTTGCTACCCTGAG (SEQ ID NO: 151) 14R CAACCATCATCTTCCACAGTC (SEQ ID NO: 152) 15 F CGGCATGAGGAAGGTGCAGGAG(SEQ ID NO: 153) 15 R CGACACCATGCGAGACACGCTTG (SEQ ID NO: 154) 16F AATGCCCAGCAGAACCGCC (SEQ ID NO: 155) 16 R ACTCCACAAACTCATCCAGGTCCTC(SEQ ID NO: 156) 17 F GCAAGATTTTTGCTTGGCTCTAT (SEQ ID NO: 157) 17R CTTTGGTATTTGCTTCCACCAAC (SEQ ID NO: 158) 18 F TGAGGCTTCACATTCCAGC(SEQ ID NO: 159) 18 R TATTCCCAGTGCTGGAGAGG (SEQ ID NO: 160) 19F TCATTGGGGCTGAGCAAT (SEQ ID NO: 161) 19 R TCAGGAGCCTTTTAGTCTGAGG(SEQ ID NO: 162) 20 F TGTTAACAATTTGCATAACAAAAGC (SEQ ID NO: 163) 20R TGATTAATTTGCGAGACTAACTTTG (SEQ ID NO: 164) 21 F GGTTCCTCCAAAGAACAGCA(SEQ ID NO: 165) 21 R TGAGATTTGGCCTTGCTTCT (SEQ ID NO: 166) 22F TCCATTGTTTACCCCAAAGC (SEQ ID NO: 167) 22 R TCTGGGAGTGGGAAGAGTTG(SEQ ID NO: 168) 23 F CCCAGCCCTCTCTCCGCC (SEQ ID NO: 169) 23R CCTAAACTGGAGACGGATCCTGCCC (SEQ ID NO: 170) 24F ACAGGCCTCCATTCATGTCCCTTCC (SEQ ID NO: 171) 24 R TCGTGGCCGCCAAGGCAC(SEQ ID NO: 172) 25 F GCATCCTATAAAAGCAGCCATGT (SEQ ID NO: 173) 25R GGCTGAGTCATCTTCCTCTTGAA (SEQ ID NO: 174) 26 F GACCATCAGGCGACAGATT(SEQ ID NO: 175) 26 R GCTCAGGCATAACCCCTC (SEQ ID NO: 176) 28F CTACCATGCCTGGCAGAAAT (SEQ ID NO: 177) 28 R TTGCTAACCTAAAAGACAGCAGG(SEQ ID NO: 178) 29 F TGAAAAGGATACCAAAGTGCG (SEQ ID NO: 179) 29R TTGGGAAATGTCAGTGACCA (SEQ ID NO: 180) 30 F GGCCAACAGGAACAGCAG(SEQ ID NO: 181) 30 R TTCTCTGGATCTTTTCAGCC (SEQ ID NO: 182) 31F CCGCGAGCTCCCTCTGCC (SEQ ID NO: 183) 31 R CTCTGTAGCCCTAGGACCGGTCTG(SEQ ID NO: 184) 32 F CTGCCGACATTCCACGGGTTTCTTG (SEQ ID NO: 185) 32R AGCCTTCCGCTGGAAGTCCAACTTT (SEQ ID NO: 186) 33 F TTTCACATTTCCTAAGCAGCC(SEQ ID NO: 187) 33 R TTGCTTTTGCCCCCACTACTG (SEQ ID NO: 188) 34F TGCCAGAGAAGTTTTAACAATCACA (SEQ ID NO: 189) 34R GGATGACAACTGCTAAGGTCCAT (SEQ ID NO: 190) 35F TATTTAAAATGTGGGCAAGATATCA (SEQ ID NO: 191) 35R TGGTGTAAATAAAGACCTTGCTATC (SEQ ID NO: 192) 38F CCATTTCGTATCAGTCTAGCCCA (SEQ ID NO: 193) 38 R GTCAGTGCTGCTATGGAGCTTTT(SEQ ID NO: 194) 41 F GCTTACTGATGAAAAACTCATCCA (SEQ ID NO: 195) 41R TGGTTATAACTAACAAACCTGAACA (SEQ ID NO: 196) 42 F CTCTATGTGGCTCACGCAG(SEQ ID NO: 197) 42 R TTTACAAATGAGGGAACTCCC (SEQ ID NO: 198) 43F TGGGAAAAGTCAGCTCGTG (SEQ ID NO: 199) 43 R AACTGGGGGCAAGAACAAC(SEQ ID NO: 200) 44 F TCATTAACACCAGTCTGCAACA (SEQ ID NO: 201) 44R TGCAATTTGAAGGTACGAGTAG (SEQ ID NO: 202) 45 F GCACCTGCTAAGGAGGGAG(SEQ ID NO: 203) 45 R TCATTTTTTGCTGATGGTTCC (SEQ ID NO: 204) 46F CCGCTGGATTCTTTTTCAAA (SEQ ID NO: 205) 46 R AAGGCTCAAATGCCAAATTG(SEQ ID NO: 206) 47 F AGCGGCCTGGATGAGATGCTG (SEQ ID NO: 207) 47R CTGGTTCACAGCCCAAAGGCTGA (SEQ ID NO: 208) 48 F CTCCCACAGACCGACCAGCTTCC(SEQ ID NO: 209) 48 R GTGCATCGTGATCTCGGGTGAGAGC (SEQ ID NO: 210) * F =forward primer, R = reverse primer ** Sequences in bold representpromoter regions *** Omitted sequential numbers indicate bad quality orfailed assays

TABLE 3 Troubleshooting Guide Problem Potential Cause SuggestedSolutions Sample well did not Confirm that single-cell contain a cellisolation process is properly dispensing a single cell per tube or wellSingle-Cell Inefficient sample lysis Use alternative lysis AmplificationCurve method or EDTA-free cell Looks Like Control collection buffer.No-Cell Cell lysate contained Do not exceed 20 mM Amplification WGAinhibitors monovalent salt Curve concentration in cell lysate Cells havebeen Handle cells without exposed to fixatives or fixation or stainingcontain dye molecules Control No-Cell DNA contamination of Carefullywash cells in Amplification Curve sample fresh PBS or other serum-Appears Early free medium Exogenous DNA Clean area thoroughly andcontamination in use PCR-dedicated sample or work plastics and pipettes.environment Reagents are Use fresh kit contaminated

REFERENCES

All patents and publications mentioned in the specification areindicative of the levels of those skilled in the art to which theinvention pertains. All patents and publications are herein incorporatedby reference in their entirety to the same extent as if each individualpublication was specifically and individually indicated to beincorporated by reference.

PATENTS

-   U.S. Pat. No. 5,759,822-   U.S. Pat. No. 6,107,023-   U.S. Pat. No. 6,114,149-   U.S. Pat. No. 6,124,120-   U.S. Pat. No. 6,280,949-   U.S. Pat. No. 6,365,375-   U.S. Ser. No. 00/551,4545A-   U.S. Ser. No. 00/593,2451A-   US20030186237A1-   WO 02/72772-   US 2003/0013671-   US2003/0017591 A1-   U.S. Ser. No. 00/627,1002B1-   US20030113754A1-   Japan Patent No. JP8173164A2-   U.S. Pat. No. 4,683,195,-   U.S. Pat. No. 4,683,202-   U.S. Pat. No. 4,800,159-   WO 90/07641-   U.S. Pat. No. 5,882,864.-   European Patent Application No. 320,308-   U.S. Pat. No. 4,883,750-   Patent Application No. PCT/US87/00880-   PCT Patent Application WO 88/10315-   U.S. Pat. No. 5,648,245-   British Patent Application No. GB 2,202,328-   PCT Patent Application No. PCT/US89/01025-   PCT Patent Application WO 89/06700-   U.S. Patent Application 20030143599-   U.S. Ser. No. 00/575,9822A-   WO/016545 A1

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Although the present invention and its advantages have been described indetail, it should be understood that various changes, substitutions andalterations can be made herein without departing from the spirit andscope of the invention as defined by the appended claims. Moreover, thescope of the present application is not intended to be limited to theparticular embodiments of the process, manufacture, composition ofmatter, means, methods and steps described in the specification. As oneof ordinary skill in the art will readily appreciate from the disclosureof the present invention, processes, manufacture, compositions ofmatter, means, methods, or steps, presently existing or later to bedeveloped that perform substantially the same function or achievesubstantially the same result as the corresponding embodiments describedherein may be utilized according to the present invention. Accordingly,the appended claims are intended to include within their scope suchprocesses, machines, manufacture, compositions of matter, means,methods, or steps.

We claim:
 1. A kit, comprising: a container; and a) a population ofprimers configured to amplify a whole genome or whole transcriptomepresent in the container, wherein the population of primers arenon-self-complementary and non-complementary to other primers in thepopulation, and comprise in a 5′ to 3′ orientation a constant region anda variable region that are adjacent to each other, wherein the constantregion sequence has a known sequence that is constant among a pluralityof primers of the population and the variable region sequence isdegenerate among the plurality of primers of the population, wherein thesequence of the constant region comprises at least 70% of two types ofnon-complementary nucleotides selected from the group consisting ofadenines and guanines; adenines and cytosines; guanines and thymidines;and cytosines and thymidines, and the sequence of the variable regioncomprises greater than 50% non-complementary nucleotides selected fromthe group consisting of adenines and guanines; adenines and cytosines;guanines and thymidines; and cytosines and thymidines; wherein theconstant region is 6-100 nucleotides in length; b) at least onetarget-specific primer for targeted amplification; c) at least onenested primer for further amplifying amplicons generated by the targetedamplification; and d) a set of instructions for using the kit to detectcopy number variation (CNV), genotype single nucleotide polymorphism(SNP), genotype micro-satellite, detect insertion and/or deletion,determine zygosity, or detect mutation(s), wherein the sequence of theconstant and variable regions will not cross-hybridize or self-hybridizeunder conditions described in the set of instructions.
 2. The kit ofclaim 1, wherein amplicons generated by the primers in (a)-(c) are atleast 100 base pairs long.
 3. The kit of claim 1, wherein the primers in(a)-(c) comprise at least 10 nucleotides.
 4. The kit of claim 1, whereinthe primers in (a)-(c) comprise at least one modified nucleotide.
 5. Thekit of claim 1, wherein melting temperature of the primers in (a)-(c) isat least 45 degrees Celsius.
 6. The kit of claim 1, wherein the at leastone nested primer is complementary to amplicons generated by thetargeted amplification.
 7. The kit of claim 1, wherein the at least onetarget-specific primer is specific to one or more target sequences. 8.The kit of claim 1, wherein the at least one target-specific primer doesnot comprise an adapter sequence.
 9. The kit of claim 1, wherein the setof instructions instructs a user to carry out a first series ofpolymerase chain reaction steps using the population of primers and theat least one target-specific primer followed by a second series ofpolymerase chain reaction steps using the at least one nested primer.10. The kit of claim 9, wherein the set of instructions furtherinstructs the user to sequence amplicons generated at the end of thesecond series of polymerase chain reaction steps using a sequencer. 11.The kit of claim 1, wherein the kit further comprises reagents selectedfrom the group consisting of a cell lysis reagent, magnesium salts, aligase, a polymerase, a reverse transcriptase, betaine and a kinase. 12.The kit of claim 1, wherein the kit is configured for use with a samplecomprising nucleic acid molecules: DNA or RNA.
 13. The kit of claim 12,wherein the sample is selected from the group consisting of blood,serum, plasma, cerebrospinal fluid, cheek scrapings, nipple aspirate,biopsy, semen, urine, feces, hair follicle, saliva, sweat,immunoprecipitated or physically isolated chromatin, a single cell or aplurality of cells.
 14. The kit of claim 12, wherein the kit isconfigured for obtaining genomic copy number, sequence information,allelic variation information, cancer diagnosis, prenatal diagnosis,paternity information, disease diagnosis, detection, monitoring, ortreatment information using the sample.
 15. The kit according to claim1, wherein the variable region comprises 4 to 20 nucleotides.
 16. A kit,comprising: a) a population of primers configured to amplify a wholegenome or whole transcriptome, wherein the population of primers arenon-self-complementary and non-complementary to other primers in thepopulation, and comprise in a 5′ to 3′ orientation a constant region anda variable region, wherein the constant region sequence has a knownsequence that is constant among a plurality of primers of the populationand the variable region sequence is degenerate among the plurality ofprimers of the population, wherein the primers of the population havesequences that are 70% or more comprised of two non-complementary andnon-self-complementary nucleotides; b) at least one target-specificprimer for targeted amplification; c) at least one nested primer forfurther amplifying amplicons generated by the targeted amplification;and d) a set of instructions for using the kit to detect copy numbervariation (CNV), genotype single nucleotide polymorphism (SNP), genotypemicro-satellite, detect insertion and/or deletion, determine zygosity,or detect mutation(s), wherein the sequence of the constant and variableregions will not cross-hybridize or self-hybridize under conditionsdescribed in the set of instructions.